Hydration of neurotransmitters: a computational and spectroscopic study of a noradrenaline analogue, 2-amino-1-phenyl-ethanol

Singly and multiply hydrated clusters of the noradrenaline analogue, 2-amino-I-phenyl-ethanol (APE) have been studied using a combination of resonant two-photon ionization time of flight spectroscopy (R2PI-TOF), infrared ion-dip spectroscopy and ab initio quantum chemical calculation. Singly hydrated clusters populate two distinct structures: the water molecule either hydrogen-bonds to the ethanol group in the extended AG conformer (leaving the intramolecular OH → N hydrogen bond intact) or inserts into the intramolecular hydrogen bond in the (distorted) ethanolamine side chain (promoting a weak NH → O bond). The observed doubly and triply hydrated clusters both display insertion structures only, with the water molecules arrayed as linear chains, hydrogen bonded to the functional groups of the side-chain and again promoting a weak NH → O bond along the distorted ethanolamine side-chain. The infrared spectrum of the 1:4 cluster of APE, which is very similar to that of the corresponding cluster of ephedrine, includes new features in the ‘window region’ (3500–3700 cm^?1), indicating the onset of a three-dimensional assembly. Comparisons with ab initio computed spectra favour a structure that incorporates a cyclic water tetramer linked to the two functional groups on the ethanolamine side-chain.     

Ab initio molecular dynamics investigations of structural, electronic and dynamical properties of water in supercritical carbon dioxide

Ab initio molecular dynamics simulations of a solitary perdeuterated water molecule solvated in supercritical carbon dioxide have been performed along an isotherm at three different densities. Electron donor-acceptor interactions between the oxygen atom of water and the carbon atom of CO₂ as well as hydrogen bonded interactions between the two molecules have been shown to play a dominant role in the solvation. The mean dipole moment of the water molecule increases with the density of the solution, from a value of 1.85 D at low density to around 2.15 D at the highest density. The increase in the solvent density causes the water molecule to exhibit a range of behavior, from a free molecule to one that interacts strongly with CO₂. A blue shift in the bending mode of water has been observed with increasing solvent density. The carbon dioxide molecules which are present in the first neighbor shell of water are found to exhibit larger propensity to deviate from a linear geometry in their instantaneous configurations.      

Effect of alkyl chain length in protic ionic liquids: an AIMD perspective

In this study we have explored, by means of ab initio molecular dynamics, a subset of three different protic ionic liquids (ILs). We present both structural and dynamical information of the liquid state of these compounds as revealed by accurate ab initio computations of the interactions. Our analysis figures out the presence of a strong hydrogen bond network in the bulk state, that is more stable in those ILs characterised by a longer alkyl side chain. Indeed it becomes more long-lasting passing from ethyl ammonium to butyl ammonium, owing to the hydrophobic effects stemming from alkyl chain contacts. Furthermore, the relative free energy landscape of the cation–anion interaction exhibits a progressively deeper well as the side chain of the cation gets longer. The hydrogen bond interaction, as already mentioned in previous works, leads to loss of degeneracy of the asymmetric stretching vibrations of the nitrate anions. The resulting frequency splitting between the two normal modes is about 90 cm^?1.     

Ab initio molecular dynamics study of aqueous formaldehyde and methanediol

The solvation shell of aqueous formaldehyde has been studied by ab initio molecular dynamics. Two different DFT approaches using BLYP and PBE functionals were explored. The results show only a slightly different mobility in the solvation shells and allow characterization of the hydrogen bonded structure with a H₂C?=?O··HOH hydrogen bond lifetime of ca. 3 ps. Formaldehyde hydrolysis was studied by following the reverse process, methanediol decomposition, by Blue Moon constrained MD showing that four water molecules are directly involved in the reaction and assisted by the whole hydration shell. The total energy of the aqueous methanediol to formaldehyde inter-conversion process is calculated with a barrier height of ca. 95?kJ?mol^?1 while the corresponding free energy barrier is only ΔG^??=?46?kJ?mol^?1 at 300?K.     

Exploring hydride-π interactions and their tuning by σ-hole bonds: an ab initio study

In the present work, ab initio calculations are performed to investigate the geometry, interaction energy and bonding properties of binary complexes formed between metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CH₃) and a series of π-acidic heteroaromatic rings. In all the resulting complexes, the heteroaromatic ring acts as a Lewis acid (electron acceptor), while the H atom of the HMX molecule acts as a Lewis base (electron donor). The nature of this interaction, called ‘hydride-π’ interaction, is explored in terms of molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. The results show that the interaction energies of these hydride-π interactions are between ?1.24 and ?2.72 kcal/mol. Furthermore, mutual influence between the hydride-π and halogen- or pnicogen-bonding interactions is studied in complexes in which these interactions coexist. For a given π-acidic ring, the formation of the pnicogen-bonding induces a larger enhancing effect on the strength of hydride-π bond than the halogen-bonding.     

Intramolecular hydrogen bonds and antioxidant activity of aminophenols

We have used IR Fourier spectroscopy to study intramolecular interactions in solutions of aminophenols in n-hexane. When the hydroxyl group in the molecule is ortho to the amino group, O-H⋯N and N-H⋯O intramolecular hydrogen bonds are formed in the aminophenols. Adding two tert-butyl groups to the benzene ring of ortho-aminophenols strengthens the O-H⋯N bond in the molecules, and prevents formation of an N-H⋯O bond. Additional acylation of the amino group in ortho-aminophenols leads to formation of an O-H⋯O=C intramolecular hydrogen bond. Formation of the above-indicated intramolecular hydrogen bonds in aminophenols affects the course of radiation-induced reactions occurring in n-hexane with participation of these compounds. The antioxidant properties of the aminophenols are enhanced when the hydroxyl groups in the molecules are found in the free state, and are diminished when strong O-H⋯N or O-H⋯O=C intramolecular hydrogen bonds are formed. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 5, pp. 577–582, September–October, 2007.     

Manifestation of intramolecular hydrogen bonds in the IR spectra of bioactive aminophenols

The intermolecular interactions in solutions of aminophenols in CCl₄ are studied by the methods of IR Fourier spectroscopy. If the hydroxyl groups of aminophenol molecules occupy the ortho positions with respect to the amino groups of the molecules, the hydroxyl and amino groups are involved in intramolecular interactions with the formation of hydrogen bonds O-H...N and N-H...O. The introduction of two additional tert-butyl groups into the structure of the aminophenol molecule facilitates the formation of O-H...N bonds and impedes the formation of N-H...O bonds. The occurrence of the carbonyl group in the structure of aminophenols leads to the formation of intramolecular hydrogen bonds O-H...O=C. The introduction of the methyl groups into carbonyl-containing aminophenols transforms the O-H...O=C bond into the hydrogen bond N-H...O=C.     

Electric dipole moment calculations of molecules with sixteen valence electrons

The field gradient fluctuation at the Li⁺ nucleus in dilute aqueous solution is calculated via Monte Carlo simulations of Li⁺ + nH₂O clusters (n = 6, 50 and 150). The intermolecular potentials and the lithium field gradient function, necessary for the simulations, are based on ab initio quantum mechanical calculations. It is found that the dominant contribution to the field gradient fluctuation at the lithium nucleus comes from the water molecules in the first shell. Furthermore, it is the lateral displacement of these molecules that causes the largest fluctuation. The contribution from the rotation of a water molecule is of minor importance. The field gradient at a lithium nucleus arising from a water molecule is badly described in a simple electrostatic model.     

Theoretical study of hydrogen adsorption in Ti-decorated capped carbon nanotube

We present ab initio study using dispersion-corrected density functional theory calculations to investigate the hydrogen interaction with Ti-coated, one end closed, single-walled carbon nanotube (SWCNT). Our results demonstrate that a single Ti atom binds up to five hydrogen molecules on SWCNT cap top, whereas adsorption of four hydrogen molecules is energetically more favourable. The analyses from adsorption energy profile, highest occupied molecular orbital–lowest unoccupied molecular orbital gap and Mulliken charge distribution show contrast in first hydrogen molecule adsorption compared with the rest of four configurations. This is clearly due to the strongly different bonding nature of first hydrogen adsorption among others, between hydrogen molecules and Ti-coated SWCNT. These results not only support our understanding of adsorption nature of hydrogen in Ti-coated SWCNTs but also suggest new directions for smart storage techniques.     

Long range C,N and H atom-atom potential parameters from ab initio dispersion energies for different azabenzene dimers

After comparing theoretically the atom-atom model with the multipole expansion for the dispersion energy, we derive atom-atom potential parameters for C, N and H contacts by fitting the atom-atom dispersion energies to the dispersion interactions calculated by an ab initio method for the following (aza)-benzene molecules: benzene, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and s-tetrazine. The data base for the fit consists of 1200 randomly chosen configurations for each azabenzene dimer. The optimized parameters for the carbon and hydrogen contacts in particular are not unique ; reasonably good fits are obtained with different parameter sets. A very simple rule, which relates the atom-atom potentials to the isotropic molecular C₆ dispersion coefficients, already leads to good estimates for the parameters. From the empirical parameter sets available in the literature the William-Govers set yields results which are close to our ab initio dispersion energies.     

Theory of hydrogen solubility in binary iron alloys based on ab initio calculation results

Interaction of hydrogen atoms with three substitutional impurities (X?=?Pd, Ti, Cr) in bcc iron base solid solution was modelled ab initio using the WIEN2k package. It was shown that in spite of attraction between H and X atoms, excess energy of the H atom in tetrahedral sites in the first sphere of coordination of the X atom has a significant positive value, while the lowest negative values are observed in the second (Pd, ?0.087?eV; Ti, ?0.091?eV) or the third (Cr, ?0.032?eV) sphere. A new thermodynamic theory of hydrogen solubility in dilute bcc Fe–X alloys was developed on the basis of these results. The resulting equation was used to analyze existing experimental data on H solubility in a number of Fe–X alloys, and X–H interaction energies were determined for each case. The energies determined from high-temperature solubility data for Fe–Pd, Fe–Ti and Fe–Cr are somewhat greater than those obtained in ab initio calculations. The theory gives a new basis for analyzing hydrogen behaviour in iron-base solid solutions.     

Concentrated Fe(III)–nitrilotriacetate solutions: study by Raman spectroscopy and ab initio calculations

Fe(III)–nitrilotriacetate(NTA) aqueous solutions are used in various redox desulfurization processes. The nature of stable Fe–NTA complexes depends highly on parameters such as [Fe(III)] concentration, NTA/Fe ratio and pH value. These complexes can be characterized by potentiometric measurements or UV‐vis spectroscopy, but only at rather low concentrations. Using synthesis of solids, Raman spectra of these solids and ab initio calculations, a rational determination of the nature of complexes stable in water at high iron concentrations was proposed from the position sensitivity of the main low wavenumber band to the coordination sphere of iron cations. This band was assigned to ν(Fe N) stretching vibrations from ab initio calculations. Depending on the pH and NTA/Fe ratio of the prepared solutions, different species were identified from the Raman spectra. The present methodology can be extended to other metal–ligand systems to elucidate the nature of stable complexes in aqueous solution. Copyright © 2006 John Wiley & Sons, Ltd.     

Symmetric bifurcated halogen bonds: substituent and cooperative effects

ABSTRACT

The aim of this study is to investigate the geometries, interaction energies and bonding properties of the symmetrical bifurcated halogen bond interactions (BXBs) by means of ab initio calculations. For this purpose, the NCX (X = Cl, Br) molecule is paired with a series of N-formyl formamide (NFF) derivatives (NFF-Z, Z = H, CN, CCH, OH, CH₃ and Li), and the properties of the resulting complexes are studied by molecular electrostatic potential, quantum theory of atoms in molecules, noncovalent interaction index and natural bond orbital analyses. For a fixed NCX molecule, interaction energies increase in the order of Z = Li > CH₃ > H > OH > CCH > CN. We found a strong correlation between the interaction energies of NCX:NFF-Z complexes and molecular electrostatic potential minimum values associated with NFF-Z monomers. Moreover, cooperative effects between BXB and X???N halogen bond interactions are studied in the ternary NCX:NCX:NFF-Z systems. Our results indicate that the strength of BXB interactions in the ternary complexes is enhanced by the presence of X???N bonds. Besides, cooperativity effects tend to increase the covalency of BXBs in these systems.     

The role of water in the design of glycosidic linkage flexibility

In this paper we show how a variety of computational methods are used to understand the role that water plays in the solution conformational dynamics of carbohydrates. A comparison is made between maltose and a designed disaccharide (α-D-Glc-NAc-(1→4)-β-D-Glc-3-NH₂) in which the cross glycosidic linkage hydrogen bonds have been significantly strengthened. However, despite the stronger intramolecular hydrogen bonds in the maltose derivative, the correlation times for glycosidic dihedral angle fluctuations are approximately the same for the two sugars. Upon investigation of the water in the first hydration shells for the two disaccharides, high water probability densities were found between the functional groups straddling the glycosidic linkage that bonds the two monosaccharides together. This probability density corresponds to single water molecules forming bridging hydrogen bonds between the functional groups on either side of the linkage for periods of 3.66 ps in the case of maltose and 8.36 ps in the case of the amine derivative. Ab initio studies of saccharide structure interaction with single water molecules reveal that these intermolecular (sugar-solvent) hydrogen bonds are of similar strength to the intramolecular (sugar-sugar) hydrogen bonds. This combination of molecular dynamics and ab initio computational methods demonstrates that increasing the internal hydrogen bond strength in oligosaccharides does not lead to significantly slower internal molecular motion of these sugars in solution. The intermolecular hydrogen bonds formed with water compete equally with the intramolecular hydrogen bonds in the sugar. This result has important implications when considering hydrophobic versus hydrophilic effects in glycoproteins.     

Studies on the structures and interactions of glutathione in aqueous solution by molecular dynamics simulations and NMR spectroscopy

All-atom molecular simulations and temperature-dependent NMR have been used to investigate the conformations and hydrogen bonds of glutathione (GSH) in aqueous solution. The simulations start from three different initial conformations. The properties are characterized by intramolecular distances, radius of gyration, root-mean-square deviation, and solvent-accessible surface. GSH is highly flexible in aqueous solutions in the simulations. Moreover, conformations can covert between “extended” and “folded” states. Interestingly, the two different hydrogen atoms in cysteine (H_N2) and glycin (H_N3) show different capabilities in forming NH?OW hydrogen bonds. The temperature-dependent NMR results of the different amide hydrogen atoms also show agreements with the MD simulations. Competing formation of GSH hydrogen-bonding interactions in aqueous solutions leads to hydrogen-bonding networks and the distribution of conformations. These changes will affect the activity of GSH under physiological conditions.     

Tuning of carbon bonds by substituent effects: an ab initio study

ABSTRACT

An ab initio study, at the MP2/aug-cc-pVTZ level of theory, is performed to study σ-hole bond in binary XH₃C···CNY complexes, where X = CN, F, NO₂, CCH and Y = H, OH, NH₂, CH₃, C₂H₅, Li. This type of interaction is labelled as ‘carbon bond’, since a covalently bonded carbon atom acts as the Lewis acid in these systems. The geometrical and energetic parameters of the resulting complexes are analysed in details. The interaction energies of these complexes are between ?4.97 kJ/mol in (HCC)H₃C···CNH and ?23.07 kJ/mol in (O₂N)H₃C···CNLi. It is found that the electrostatic interaction plays a key role in the overall stabilisation of these carbon-bonded complexes. To deepen the understanding of the nature of the carbon-bonding, the molecular electrostatic potential, natural bond orbital, quantum theory of atoms in molecules and non-covalent interaction index analyses are also used. Our results indicate that the carbon bond is favoured over the C-H···C hydrogen bond in the all complexes considered and may suggest the possible important roles of the C···C interactions in the crystal growth and design.     

Investigation of inter-molecular hydrogen bonding in the binary mixture (acetone + water) by concentration dependent Raman study and ab initio calculations

This paper reports that vibrational spectroscopic analysis on hydrogen-bonding between acetone and water comprises both experimental Raman spectra and ab initio calculations on structures of various acetone/water complexes with changing water concentrations. The optimised geometries and wavenumbers of the neat acetone molecule and its complexes are calculated by using ab initio method at the MP2 level with 6-311+G(d,p) basis set. Changes in wavenumber position and linewidth (fullwidth at half maximum) have been explained for neat as well as binary mixtures with different mole fractions of the reference system, acetone, in terms of intermolecular hydrogen bonding. The combination of experimental Raman data with ab initio calculation leads to a better knowledge of the concentration dependent changes in the spectral features in terms of hydrogen bonding.     

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

The properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller–Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.     

A density functional theory and quantum theory of atoms in molecules study on hydrogen bonding interaction between paracetamol and water molecules

To consider the hydrogen bonding interactions between paracetamol and water molecules, probable complexes of paracetamol from three active sites (carbonyl oxygen atom, hydroxyl oxygen atom, and nitrogen atom) with H₂O molecule were formed. The optimized geometries and total energies have been obtained at the B3PW91/6-31+G(d, p) level of theory. Comparison of hydrogen bond lengths and the energies of complexes showed hydrogen bond that form between the oxygen atom of the carbonyl group and hydrogen atom is stronger than others. Moreover, an increase in the number of hydrogen bonds increases stability of paracetamol-water complexes. At the end, the QTAIM was applied to explain the nature of the hydrogen bonds and confirm the more stability by complexation.