Steric control over hydrogen bonding in crystalline organic solids: a structural study of N,N'-dialkylthioureas

Hydrogen bonding in crystalline N,N'-dialkylthioureas was examined with the help of single-crystal X-ray diffraction, DFT calculations, and Cambridge Structural Database (CSD) analysis. A CSD survey indicated that unlike the related urea derivatives, which persistently self-assemble into one-dimensional hydrogen-bonded chains, the analogous thioureas can form two different hydrogen-bonding motifs in the solid state: chains, structurally similar with those found in ureas, and dimers, that further associate into hydrogen-bonded layers. The formation of one motif or another can be manipulated by the bulkiness of the organic substituents on the thiourea group, which provides a clear example of steric control over the hydrogen bonding arrangement in crystalline organic solids.     

Studies in hydrogen bonding: Association in ammonia using an empirical potential

The empirical potential EPEN /2 has been used to establish the structures of isolated hydrogen-bonding ammonia clusters. The most stable forms of the dimer have a linear or near-linear structure. The trimer has a closed structure with zero dipole moment. Two stable tetramer forms were found: one with a closed structure and zero dipole moment in agreement with experimental findings, and one with a pyramidal structure with nonzero dipole moment which may be an artifact of the EPEN /2 potential. The relation of the dimer structures to the limited available experimental information is discussed.     

Studies in hydrogen bonding: Association within mixed dimers of water,methanol, ammonia,and methylamine using the empirical potential EPEN

An empirical potential EPEN has been used to find the stable geometries and approximate hydrogenbond energies of the mixed dimers formed between molecules of water, methanol, ammonia, and methylamine. These results are compared with results in the literature obtained using ab initio methods.     

On the hydrogen bonding between water and ammonia molecules

The hydrogen bond N·HO between the water and ammonia molecules has been investigated ab initio using the SCF LCAO MO method. The minimal and extended basis sets of Slater type orbitals were used. It was found that the energy of the hydrogen bond is equal to 6.44 kcal/mole and the equilibrium separation of the oxygen and nitrogen atoms in the dimer is 5.72 au. At this intermolecular distance there is only one minimum in the potential energy curve for the motion of proton.     

Studies in hydrogen bonding: Association within small clusters of water,methanol, and ammonia molecules using Jorgensen's intermolecular pair potentials

The geometries of the dimer, trimer, and tetramer hydrogen-bonded clusters of water, methanol, and ammonia molecules have been derived using previously published intermolecular pair potentials containing constants optimized from ab initio calculations. The lowest energy forms for the dimers of all three types of molecules have an open structure, while the trimers and tetramers have cyclic structures. The results are compared with those previously described using another empirical potential, EPEN .     

Computer simulation of the 13 crystalline phases of ice

As a reference for follow-up studies toward more accurate model parametrizations, we performed molecular-dynamics and Monte Carlo simulations for all known crystalline phases of ice, as described by the simple point-charge/extended and TIP4P water models. We started from the measured structures, densities, and temperatures, and carried out classical canonical simulations for all these arrangements. All simulated samples were cooled down close to 0 K to facilitate the comparison with theoretical estimates. We determined configurational internal energies as well as pressures, and monitored how accurately the measured configurations were preserved during the simulations. While these two models predicted very similar thermophysical and structural properties for water at ambient conditions, the predicted features for the corresponding ice polymorphs may differ significantly.     

First principles molecular dynamics study of filled ice hydrogen hydrate

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and∕or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and∕or low temperatures.     

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

Quantum studies of hydrogen bonding in formic acid and water ice surface

The structure and spectroscopy (electronic and vibrational) of formic acid (HCOOH) dimers and trimers are investigated by means of the hybrid (B3LYP) density-functional theory. Adsorption of single and dimer HCOOH on amorphous water ice surface is modeled using two different water clusters. Particular attention has been given to spectroscopic consequences. Several hypotheses on formic acid film growing on ice and incorporation of a single water molecule in the formic acid film are proposed.     

Investigation of the hydrogen bonding in ice Ih by first-principles density function methods

It is a well recognized difficult task to simulate the vibrational dynamics of ices using the density functional theory (DFT), and there has thus been rather limited success in modelling the inelastic neutron scattering (INS) spectra for even the simplest structure of ice, ice Ih, particularly in the translational region below 400 cm(-1). The reason is partly due to the complex nature of hydrogen bonding (H-bond) among water-water molecules which require considerable improvement of the quantum mechanical simulation methods, and partly owing to the randomness of protons in ice structures which often requires simulation of large super-lattices. In this report, we present the first series of successful simulation results for ice Ih using DFT methods. On the basis of the recent advancement in the DFT programs, we have achieved for the first time theoretical outcomes that not only reproduce the rotational frequencies between 500 to 1200 cm(-1) for ice Ih, but also the two optic peaks at ～240 and 320 cm(-1) in the translational region of the INS spectra [J. C. Li, J. Chem. Phys 105, 6733 (1996)]. Besides, we have also investigated the impact of pairwise configurations of H(2)O molecules on the H-bond and found that different proton arrangements of pairwise H(2)O in the ice Ih crystal lattice could not alter the nature of H-bond as significantly as suggested in an early paper [J. C. Li and D. K. Ross, Nature (London) 365, 327 (1993)], i.e., reproducing the two experimental optic peaks do not need to invoke the two H-bonds as proposed in the previous model which led to considerable debates. The results of this work suggest that the observed optic peaks may be attributed to the coupling between the two bands of H-O stretching modes in H(2)O. The current computational work is expected to shed new light on the nature of the H-bonds in water, and in addition to offer a new approach towards probing the interaction between water and biomaterials for which H-bond is essential.     

Supramolecular main-chain liquid crystalline polymers and networks with competitive hydrogen bonding

A series of supramolecular polymers and networks with variable liquid crystalline characteristics have been created. These species are formed though the benzoic acid/pyridine associations of a flexible bisacid and a mixture of a rigid bispyridyl and a non-mesogenic tetrapyridyl. The networked systems displayed liquid crystalline characteristics up to and including 22.5% netpoint inclusion. Above this concentration, only crystalline and melting behaviours were observed. This observed phenomenon would seem to be linked to the statistical correlation of hydrogen bond acceptors and donors. There was also no observed phase segregation of the species after multiple heat/cool cycles and extended periods of time in the isotropic state. This would indicate that the thermodynamically more stable mesogenic phase cannot out-compete the non-liquid crystalline network. Computational analysis indicates no significant difference in hydrogen bond strength between the two different hydrogen bond acceptors.     

Studies of intramolecular hydrogen bonding in protonated and non-protonated hexahydropyridinobenzodioxins

The conformational stability of hexahydropyridobenzodioxin and related derivatives in both protonated and non-protonated forms have been investigated by means of ab initio molecular orbital methods as well as semi-empirical AM1 and PM3 methods. One of the cis conformers (cis2e) has been found to be most stable due to the formation of an intramolecular hydrogen bond, other conformers including the trans isomer cannot form this interaction but are of different stability because of the orientation of the polar oxygens and the nitrogen. The effect of the intramolecular hydrogen bonding on the stability of hexahydropyridobenzodioxin and its methylated derivatives has been examined using various basis sets levels. In protonated form, both the semi-empirical and ab initio calculations give excellent agreement in energetic order; however, different orderings of conformer stabilities are observed by different computational methods in non-protonated form. The results provide insight into the intramolecular hydrogen bonding in computational studies of biologically important molecules.     

Self-assembly of main chain liquid crystalline polymers via heteromeric hydrogen bonding

Complexation between pyridines and carboxylic acids is driven by hydrogen bonding. This simple, single hydrogen bond is shown to be capable of serving concomitantly as both the agent of liquid crystallinity and as the coupling bond generating an extended linear chain structure. Three such complexes made from an aromatic diacid and three structurally different bis pyridyls were prepared. In each case the association complex self-assembles into an organized liquid crystalline phase. Discussion of this complexation as a step-growth polymerization process is presented along with an examination of the suitability of various methods for characterizing these materials.     

Study of hydrogen bonding in liquid crystalline solvent by Fourier transform infrared spectroscopy

A hydrogen-bonded complex between an aromatic acid and an enantiopure chiral amine has been dissolved in a nematic solvent, giving rise to a cholesteric medium. Fourier transform infrared (FT-IR) experiments have been performed at various temperatures on both sides of the cholesteric-isotropic transition. Liquid crystalline order provides significant enhancement to the strength of interaction, inducing a discontinuous jump in concentration of the complex at the cholesteric-isotropic transition.     

Pressure and temperature dependence of the hydrogen bonding in supercritical ethanol: a computer simulation study

As a step toward deeper insight on the "hydrogen bonding" in supercritical ethanol (scEtOH), we carried out NVT molecular dynamics simulations of the fluid over a wide range of temperatures and pressures. The fluid was studied at SC conditions for which thermodynamic and spectroscopic (NMR, infrared, Raman, dielectric) data are available. The various site-site pair distribution functions (pdf's) were calculated, and their temperature and pressure dependence was obtained. It was found that over the thermodynamic conditions investigated here, scEtOH remains highly structured. Moreover, the characteristic behavior of the first peaks in H-H, O-O, and H-O pdf's reveals that hydrogen bonds still exist in scEtOH. The analysis focuses also on the reorientational dynamics of the bond unit vectors O-H, C-O, and of the permanent dipole moment of the molecules as well as the total dipole moment of the sample. The corresponding Legendre time correlation functions were discussed in connection to the "hydrogen bonding" in the fluid and in the context of experimental results. Specifically, the behavior of the O-H dynamics exhibits the well-known associative nature of the molecules in the system. A further analysis of the hydrogen bonds was carried out, and the degree of aggregation (average number of H-bonds per molecule) was obtained and compared with results from NMR chemical shift studies. Also the estimated monomer and free O-H groups in the fluid were compared with results from IR and Raman vibrational spectroscopy. The percentage analysis fi of the liquid and scEtOH molecules, with i = 0, 1, 2, 3, ... hydrogen bonds per molecule, has been obtained. The results show the existence of small, linear-chain oligomers formed mainly by two molecules, whereas the number of the three body oligomers, and specifically that of four body oligomers in the sample, is relatively small.     

Studies in hydrogen bonding: Association in methanol using an empirical potential

The empirical potential, EPEN , has been used to establish the structures of isolated hydrogen-bonded clusters in methanol. The most stable configuration of the dimer is found to have a trans near-linear form, whereas the most stable forms of the trimer and tetramer are cyclic. Charge interactions in the tetramer make it the most stable, in terms of energy per hydrogen bond, of these three species. These results are in conformity with various types of experiment. Other species of dimer, trimer, and tetramer, corresponding to local energy minima, have also been identified.     

Studies on the hydrogen bonding of aniline's derivatives by FT-IR

The hydrogen bonding of 23 aniline's derivatives in various solvents and in solid states are studied by Fourier transform infrared spectroscopy. The Infrared absorption of their amino group is greatly influenced by solvents. Compared with those data determined in hexane, the symmetric stretching frequency (nu(s)) and asymmetric stretching frequency (nu(as)) of amino group have an obvious bathochromic shift in benzene, but a relatively smaller shift in CCl4. It is also found that the concentration of these compounds has very little effect on the frequencies, the band shapes and relative absorption intensities of amino group. This indicates that the intermolecular hydrogen bonds are very weak between the aniline's derivatives in the solution. The substituent of methyl (-CH3) has different electronic effects in organic solvents with various polarities. Methyl group behaves as an electron-donating functional group in hexane, however, it shows an electron-withdrawing effect in benzene. When methoxyl (CH3O-) is ortho-substituted, v(as) of amino group increases and nu(s) almost does not change. While methoxyl (CH3O-) is meta-substituted, v(as) of amino group increases, but nu(s) decreases. The groups of chloro- (Cl-) and nitro- (-NO2) cause a hyposochromic shift of the nu(as) and nu(s) of amino group, while substituent of -NH2 makes a bathochromic shift. The solvents influence the relative intensities of nu(as) and nu(s) of amino group more greatly than the substituents do. In solid states, the amino group of aniline's derivatives has more than two absorption bands because of forming the inter- or intra-molecular hydrogen bonds.     

Quantum chemical simulation of the mechanism of ammonia hydrate formation in low-temperature crystallization under reduced pressure

The quantum chemical calculation of thermodynamic and energy parameters of crystalline hydrates of ammonia was performed by the B3LYP/6-31+G(d) method. The calculated structural parameters, activation energies, and full energies confirm the conclusion about the formation of ammonia crystalline hydrates in low-temperature crystallization under reduced pressure.     

Raman study of the temperature and pressure effects on the Fermi resonance and hydrogen bonding in liquid ammonia

The Raman bands of ammonia, v₁ and 2v₄ vibrations coupled by Fermi resonance, have been studied at pressures varied from vapour pressure up to 2 kbar and over a temperature range from 0 to 100°C. The Fermi parameters of the uncoupled frequencies Ω_a and Ω_b, the intensity ratios of the bands in resonance, R, and the anharmonic force constant,f₁₄₄, have been obtained by using standard procedures and also by fitting the isotropic spectra to the coupled oscillator functions. The internally consistent results have been compared to the previously published data and discussed in terms of the hydrogen bonding interactions. The spectroscopic results indicate that no additional band due to hydrogen bonding is present in the Raman spectrum.