Adsorption of Choline Phenylalanilate on Polyaromatic Hydrocarbon-Shaped Graphene and Reaction Mechanism with CO2: A Computational Study.

The interaction of ionic liquids (ILs) with carbon materials is of fundamental importance in several areas of materials science, physics, and chemistry. Their adsorption on pristine and N-doped graphene surfaces is discussed here on the basis of results of density functional theory calculations. The nature of adsorption was investigated for an amino acid (AA)-based IL consisting of the choline cation [Ch] and the l-phenylalanilate anion [Phe] that interacts with a sheet of N-doped graphene. The interaction mechanism, binding energy, electron density, and non-covalent interaction analysis were evaluated by considering the cation, anion, and ion pair adsorbed on graphene separately. The distribution of cations and anions in the liquid bulk and on the graphene surface was then analyzed by molecular dynamics simulations. Since AA-based ILs are efficient absorbents for capture of CO2 due to the pronounced affinity of carbon dioxide to react with amino groups, we investigated the capacity of [Ch][Phe] to react with CO2 under various conditions. We considered the multistep mechanism of the reaction of [Phe] with CO2 first for the anion in the liquid bulk and then for the [Phe] anion adsorbed on the graphene surface. The initial step, the formation of the zwitterionic addition product, is followed by its structural rearrangement through intramolecular proton transfer and conformational isomerization processes to form carboxylic acid derivatives. The entire mechanism was evaluated for the [Phe] anion before and after adsorption on graphene to investigate how interactions with surfaces of carbon materials can affect the CO2 capture capacity of an AA-based IL such as [Ch][Phe].

Reaction Mechanism of CO2 with Choline-Amino Acid Ionic Liquids: A Computational Study.

Carbon capture and sequestration are the major applied techniques for mitigating CO2 emission. The marked affinity of carbon dioxide to react with amino groups is well known, and the amine scrubbing process is the most widespread technology. Among various compounds and solutions containing amine groups, in biodegradability and biocompatibility perspectives, amino acid ionic liquids (AAILs) are a very promising class of materials having good CO2 absorption capacity. The reaction of amines with CO2 follows a multi-step mechanism where the initial pathway is the formation of the C-N bond between the NH2 group and CO2. The added product has a zwitterionic character and can rearrange to give a carbamic derivative. These steps of the mechanism have been investigated in the present study by quantum mechanical methods by considering three ILs where amino acid anions are coupled with choline cations. Glycinate, L-phenylalanilate and L-prolinate anions have been compared with the aim of examining if different local structural properties of the amine group can affect some fundamental steps of the CO2 absorption mechanism. All reaction pathways have been studied by DFT methods considering, first, isolated anions in a vacuum as well as in a liquid continuum environment. Subsequently, the role of specific interactions of the anion with a choline cation has been investigated, analyzing the mechanism of the amine-CO2 reaction, including different coupling anion-cation structures. The overall reaction is exothermic for the three anions in all models adopted; however, the presence of the solvent, described by a continuum medium as well as by models, including specific cation- -anion interactions, modifies the values of the reaction energies of each step. In particular, both reaction steps, the addition of CO2 to form the zwitterionic complex and its subsequent rearrangement, are affected by the presence of the solvent. The reaction enthalpies for the three systems are indeed found comparable in the models, including solvent effects.

Choline Hydrogen Dicarboxylate Ionic Liquids by X-ray Scattering, Vibrational Spectroscopy and Molecular Dynamics: H-Fumarate and H-Maleate and Their Conformations.

We explore the structure of two ionic liquids based on the choline cation and the monoanion of the maleic acid. We consider two isomers of the anion (H-maleate, the cis-isomer and H-fumarate, the trans-isomer) having different physical chemical properties. H-maleate assumes a closed structure and forms a strong intramolecular hydrogen bond whereas H-fumarate has an open structure. X-ray diffraction, infrared and Raman spectroscopy and molecular dynamics have been used to provide a reliable picture of the interactions which characterize the structure of the fluids. All calculations indicate that the choline cation prefers to connect mainly to the carboxylate group through OH⋯O interactions in both the compounds and orient the charged head N(CH3)3+ toward the negative portion of the anion. However, the different structure of the two anions affects the distribution of the ionic components in the fluid. The trans conformation of H-fumarate allows further interactions between anions through COOH and CO2- groups whereas intramolecular hydrogen bonding in H-maleate prevents this association. Our theoretical findings have been validated by comparing them with experimental X-ray data and infrared and Raman spectra.

Reducing Properties of Superalkalis on Pyridinic Graphene Surfaces: a Computational Study.

The hyperlithiated species Li k + 1 F k (k=1, 2, 3, and 4) have been studied by quantum mechanical (QM) methods. Different structures have been localized for each molecule by the CBS-QB3 composite method: all the isomers show superalkali properties and strong tendency to donate an electron to carbon dioxide forming stable Li k + 1 F k · · · CO 2 complexes. With the aim to find molecular systems able to stabilize superalkalis, geometries of complexes between superalkalis and pyridine and superalkalis and graphene surfaces doped with a pyridinic vacancy were calculated. The pyridinic graphene sheets were modeled with two finite molecular systems C69 H21 N3 and C117 H27 N3 . The interaction with one pyridine molecule is quite weak and the superalkali maintains its structure and electron properties. The affinity for graphene sheets is instead stronger and the superalkalis tend to deform their geometry to better interact with the graphene surface. However, the superalkalis continue to show the tendency to transfer electrons to carbon dioxide reducing CO2 , as found in graphene absence.

Coupled hydroxyl and ether functionalisation in EAN derivatives: the effect of hydrogen bond donor/acceptor groups on the structural heterogeneity studied with X-ray diffractions and fixed charge/polarizable simulations.

We present a study by energy-dispersive X-ray diffraction of liquid 2-(2-hydroxyethoxy)ethan-1-ammonium nitrate, NH3CH2CH2(OCH2CH2OH)+NO3- (22HHEAN). This ionic liquid is derived from the parent ethylammonium nitrate (EAN) with an ether link in the chain and a hydroxyl group in the terminal position. The absence of peaks at low-q values in the experimental diffraction curve indicates that the added polar groups and the high conformational isomerism of the cations alter strongly the nanosegregation of the parent EAN liquid. Aggregation between ionic species may involve hydrogen bonding between cations and anions and a variety of intermolecular hydrogen bonds between cations. Diffraction patterns are compared with the results of molecular dynamics simulations with two different force fields: the fixed point charge force field (GAFF) with different charge scaling protocols and the polarizable AMOEBA force field. Most point charge models lead to the appearance of a quite evident low q-peak which decreases gradually, when the percentage and type of the scaling (uniform vs. non-uniform) are increased. In the polarisable model and in the model where only anion charges are scaled to 20%, instead, the pre-peak is absent in agreement with our experiments.

Peroxy self-reaction leading to the formation of furfural.

Interest in alternative fuels to petroleum and classical fuels has been growing very rapidly in recent years. Furan and its alkyl derivatives, such as methylfuran (2MF), have been identified as valid alternative biofuels. This study focuses on the self-reaction of the peroxy radical generated in the first oxidation step of 2MF, initiated by Cl atoms at 323 K and 4 Torr. The experiments have been carried out by a multiplexed synchrotron photoionization mass spectrometer (mSPIMS) at the Advanced Light Source (ALS) of Lawrence Berkeley National Laboratory (USA). The presence of a peak at m/z = 96 reveals that furfural is the dominant product of 2MF oxidation. Various reaction mechanisms for furfural formation are proposed here. The potential energy surfaces for singlet and triplet spin states have been mapped using quantum mechanical methods, such as CCSD(T), DFT-B3LYP, and composites models (CBS-QB3), to optimize the products, transition states, and intermediates. Experimental and theoretical results provide evidence that furfural does not form by primary reaction chemistry. Self-reaction of the peroxy radical generated in the first oxidation step of 2MF has been proposed as the pathway leading to the formation of furfural. Among various reaction channels, we indentified some entirely exothermic pathways involving oxygen-oxygen coupling and the formation of ROOOOR Russell intermediates.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Vibrations of bioionic liquids by ab initio molecular dynamics and vibrational spectroscopy.

Density functional theory and vibrational spectroscopy are used to investigate a class of bioionic liquids consisting of a choline cation and carboxylate anions. Through quantum mechanical studies of motionless ion pairs and molecular dynamics of small portions of the liquid, we have characterized important structural features of the ionic liquid. Hydrogen bonding produces stable ion pairs in the liquid and induces vibrational features of the carboxylate groups comparable with experimental results. Infrared and Raman spectra of liquids have been measured, and main bands have been assigned on the basis of theoretical spectra.

Glycine in 1-butyl-3-methylimidazolium acetate and trifluoroacetate ionic liquids: effect of fluorination and hydrogen bonding.

The solvation of glycine in two ionic liquids (ILs), namely, 1-butyl-3-methylimidazolium acetate, [C(1)C(4)Im][OAc], and 1-butyl-3-methylimidazolium trifluoroacetate, [C(1)C(4)Im][TFA], was studied by a combination of experimental and theoretical methods. The solubility of glycine in both ILs was determined at 333.15 K to be (8.1±0.5) and (1.0±0.5) wt % in [C(1)C(4)Im][OAc] and [C(1)C(4)Im][TFA], respectively. By IR spectroscopy it was found that, when dissolved in the ILs, glycine was mainly present in its zwitterionic form. Structural and energetic aspects of the solvation of glycine in the ILs and in mixtures of ILs and water were investigated by ab initio calculations and molecular dynamic simulations. It was observed that the firstly solvation shell around glycine consisted predominantly of acetate or trifluoroacetate anions, which formed hydrogen bonds either with the carboxylic group of neutral glycine or with the protonated ammonium group of the zwitterionic form. When water is present in the solutions, hydrogen bonds between water and the anion prevail. The overall energy of the system was decomposed into its components between pairs of species. It was established that the dominant contribution to the interaction energy between glycine and the IL was due to hydrogen bonds with the anions and the statistics of hydrogen bonds were analysed.

Transmission of electronic substituent effects through a benzene framework: a computational study of 4-substituted biphenyls based on structural variation.

The transmission of substituent effects through a benzene framework has been studied by a novel approach, based on the structural variation of the Ph group in p-Ph-C(6)H(4)-X molecules. The molecular structures of many 4-substituted biphenyls were determined from MO calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. The twist angle between the phenyl probe (ring B) and the benzene framework carrying the substituent (ring A) was set at 90° to prevent π-electron transfer from one ring to the other and at 0° to maximize it. The structural variation of the probe is best represented by a linear combination of the internal ring angles, termed S(F)(BIPH(o)) and S(F)(BIPH(c)) for the orthogonal and coplanar conformations of the molecules, respectively. Regression analysis of these parameters using appropriate explanatory variables reveals a composite field effect, a substantial proportion of which is originated by resonance-induced π-charges on the carbon atoms of ring A. Field-induced polarization of the π-system of ring A also contributes to the structural variation of the probe. Thus, the S(F)(BIPH(o)) parameter is very well reproduced by a linear combination of the π-charges on the ortho, meta, and para carbons of ring A, an uncommon example of a quantitative relationship between molecular geometry and electron density distribution. Comparison of S(F)(BIPH(o)) with the gas-phase acidities of para-substituted benzoic acids shows that, while the deprotonating carboxylic probe is more sensitive to π-electron withdrawal than donation, the phenyl probe is equally sensitive to both. While the ability of the orthogonal biphenyl system to exchange π-electrons with the para substituent is the same as that of the benzene ring in Ph-X molecules, an increase by about 18% occurs when the conformation is changed from orthogonal to coplanar. The structural variation of the probe becomes more complicated, however. This is due to π-electron transfer from one ring to the other, which is shown to introduce quadratic terms in the regressions.

Vibrational spectra of water solutions of azoles from QM/MM calculations: effects of solvation.

Using microsolvation models and mixed quantum/classical ab initio molecular dynamics simulations, we investigate the vibrational properties of two azoles in water solution: pyrazole and oxazole. The effects of the water-azole hydrogen bonding are rationalized by an extensive comparison between structural parameters and harmonic frequencies obtained by microsolvation models. Following the effective normal-mode analysis introduced by Martinez et al. [Martinez et al., J. Chem. Phys. 2006, 125, 144106], we identify the vibrational frequencies of the solutes using the decomposition of the vibrational density of states of the gas phase and solution dynamics. The calculated shifts from gas phase to solution are fairly in agreement with the available experimental data.

Liquid structure of 1-alkyl-3-methylimidazolium-hexafluorophosphates by wide angle x-ray and neutron scattering and molecular dynamics.

We report for the first time joined energy dispersed x-ray and neutron diffraction experiments on a series of (both protiated and selectively deuteriated) 1-alkyl-3-methylimidazolium hexafluorophosphate salts (alkyl = butyl, hexyl, octyl) at ambient conditions. The x-ray experimental data are used to optimize the interaction potential used for running molecular dynamics simulations on these systems. Such a potential leads to a good description of neutron scattering data from the samples without additional refinement, thus further validating the potential definition. The molecular dynamics simulations were used to access microscopic information on the morphology of the proposed systems, thus probing the role played by alkyl chain length on the structure. The comparison of x-ray weighted and neutron-weighted computed diffraction patterns allows the rationalization of several diffraction features. Further insight into cation-anion coordination and alkyl chain conformational equilibrium is provided on the basis of the MD-derived snapshots, confirming and extending previously obtained results on these issues.

Electronic substituent effects in bicyclo[1.1.1]pentane and [n]staffane derivatives: a quantum chemical study based on structural variation.

The transmission of electronic substituent effects through one or more bicyclo[1.1.1]pentane units has been investigated by ascertaining how a variable substituent at a bridgehead position perturbs the geometry of a phenyl group at the opposite end of the molecule. We have analyzed the molecular structures of many bicyclo[1.1.1]pentane and [n]staffane derivatives of general formula Ph-[C(CH(2))(3)C](n)-X (n = 1-5), as obtained from molecular orbital calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. When n = 1, the structural variation of the benzene ring is controlled primarily by the long-range polar effect of X, with significant contributions from electronegativity and pi-transfer effects. The capability of the bicyclo[1.1.1]pentane framework to transmit these short-range effects originates from the rather high electron density inside the cage and the hyperconjugative interactions occurring between substituent and framework. A set of at least two bicyclo[1.1.1]pentane units appears to be necessary to remove most of the electronegativity and pi-transfer effects. In higher [n]staffanes (n >or= 3), the very small variation of the benzene ring geometry is controlled entirely by the long-range polar effect of X. With charged groups and for n >or= 2, the potential energy of the ring deformation decreases linearly with n(-3). In Ph-C(CH(2))(3)C-X molecules, the relatively large deformation of the bicyclo[1.1.1]pentane cage is determined primarily by the electronegativity of X, similar to the electronegativity distortion of the benzene ring in Ph-X molecules. Transfer of pi electrons from substituent to cage or vice versa also plays a role in determining the cage deformation.

Hydration of diazoles in water solution: pyrazole. A theoretical and X-ray diffraction study.

The local structure of the hydration of pyrazole has been analysed through static and dynamical microsolvation models described by quantum mechanical methods. Then, a reliable classical force field of pyrazole has been obtained on the basis of the quantum mechanical results and the dynamical properties of aqueous pyrazole solutions have been studied by molecular dynamics simulations. Finally, the structure of pyrazole-water solutions at different concentrations has been investigated by energy dispersive X-ray diffraction and experimental results have been compared to calculations. This comparison provides both a tool for interpretation of experiments and a way to validate the computational protocol.

Molecular structure and benzene ring deformation of three cyanobenzenes from gas-phase electron diffraction and quantum chemical calculations.

The molecular structures of cyanobenzene, p-dicyanobenzene, and 1,2,4,5-tetracyanobenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations. The equilibrium structures of these molecules are planar, but their average geometries in the gaseous phase are nonplanar because of large-amplitude vibrational motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in electron diffraction analysis is necessary to yield ring angles consistent with the results of MO calculations. The angular deformation of the benzene ring in the three molecules is found to be much smaller than obtained from previous electron diffraction studies, as well as from microwave spectroscopy studies of cyanobenzene. While the deformation of the ring CC bonds and CCC angles in p-dicyanobenzene is well interpreted as arising from the superposition of independent effects from each substituent, considerable deviation from additivity occurs in 1,2,4,5-tetracyanobenzene. The changes in the ring geometry and C ipso-C cyano bond lengths in this molecule indicate an enhanced ability of the cyano group to withdraw pi-electrons from the benzene ring, compared with cyanobenzene and p-dicyanobenzene. In particular, gas-phase electron diffraction and MP2 or B3LYP calculations show a small but consistent increase in the mean length of the ring CC bonds for each cyano group and a further increase in 1,2,4,5-tetracyanobenzene. Comparison with accurate results from X-ray and neutron crystallography indicates that in p-dicyanobenzene the internal ring angle at the place of substitution opens slightly as the molecule is frozen in the crystal. The small geometrical change, about 0.6 degrees , is shown to be real and to originate from intermolecular C identical withN...HC interactions in the solid state.

Inhomogeneity in Ethylammonium Nitrate-Acetonitrile Binary Mixtures: The Highest "Low q Excess" Reported to Date.

The binary mixtures of the ionic liquid ethylammonium nitrate with acetonitrile have been studied by means of wide- and small-angle X-ray scattering and via two different computational methods, namely, classical molecular dynamics and DFT. The recently debated odd feature in the extreme low q region of some ionic liquid-based binary mixtures is linked to density fluctuations within the system. We show how the "low q excess" is due to some nanoscopic objects which are formed at certain compositions. These structures have different density with respect to the surrounding, thus generating the feature observed. Our results also show how the local arrangement is directly linked to the long-range structure. Moreover, we found once again a similarity in the physicochemical behavior of ethylammonium nitrate and water.

Liquid structure of 1-ethyl-3-methylimidazolium alkyl sulfates by X-ray scattering and molecular dynamics.

We report a joined X-ray diffraction and molecular dynamics study on the series of 1-ethyl-3-methylimidazolium alkyl sulfates (alkyl = ethyl, butyl, hexyl, octyl) ionic liquids. A general good agreement between experimental and theoretical structure functions has been found for each term of the series in all ranges of q values. Once the quality of the employed force field in reproducing structural data was tested, we used dynamics simulations to access information on morphology and properties of these systems. The series of ionic liquids presents nanoscale structural heterogeneity, whose size depends on the anion alkyl chain size. Analyzing our simulation data on the basis of alkyl chain length, we propose a structural model consistent with the presence of low q peaks.

Dimerisation of urea in water solution: a quantum mechanical investigation.

The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.

Polar effects and structural variation in 4-substituted 1-phenylbicyclo[2.2.2]octane derivatives: a quantum chemical study.

The transmission of polar effects through the bicyclo[2.2.2]octane framework has been investigated by ascertaining how the geometry of a phenyl group at a bridgehead position is affected by a variable substituent at the opposite bridgehead position. We have determined the molecular structure of several Ph-C(CH(2)-CH(2))(3)C-X molecules (where X is a charged or dipolar substituent) from HF/6-31G and B3LYP/6-311++G molecular orbital calculations and have progressively replaced each of the three -CH(2)-CH(2)- bridges by a pair of hydrogen atoms. Thus the bicyclo[2.2.2]octane derivatives were changed first into cyclohexane derivatives in the boat conformation, then into n-butane derivatives in the anti-syn-anti conformation, and eventually into assemblies of two molecules, Ph-CH(3) and CH(3)-X, appropriately oriented and kept at a fixed distance. For each variable substituent the deformation of the benzene ring relative to X = H remains substantially the same even when the substituent and the phenyl group are no longer connected by covalent bonds. This provides unequivocal evidence that long-range polar effects in bicyclo[2.2.2]octane derivatives are actually field effects, being transmitted through space rather than through bonds. Varying the substituent X in a series of Ph-C(CH(2)-CH(2))(3)C-X molecules gives rise to geometrical variation (relative to X = H) not only in the benzene ring but also in the bicyclo[2.2.2]octane cage. The two deformations are poorly correlated. The rather small deformation of the benzene ring correlates well with traditional measures of long-range polar effects in bicyclo[2.2.2]octane derivatives, such as sigma(F) or sigma(I) values. The much larger deformation of the bicyclo[2.2.2]octane cage is controlled primarily by the electronegativity of X, similar to deformation of the benzene ring in Ph-X molecules. Thus the field and electronegativity effects of the substituent are well separated and can be studied simultaneously, as they act on different parts of the molecular skeleton.

Molecular structure and benzene ring deformation of three ethynylbenzenes from gas-phase electron diffraction and quantum chemical calculations.

The molecular structures of ethynylbenzene and s-triethynylbenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations and are compared to that of p-diethynylbenzene from a previous study [Domenicano, A.; Arcadi, A.; Ramondo, F.; Campanelli, A. R.; Portalone, G.; Schultz, G.; Hargittai, I. J. Phys. Chem. 1996, 100, 14625]. Although the equilibrium structures of the three molecules have C2v, D3h, and D2h symmetry, respectively, the corresponding average structures in the gaseous phase are best described by nonplanar models of Cs, C3v, and C2v symmetry, respectively. The lowering of symmetry is due to the large-amplitude motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in the electron diffraction analysis yields ring angles consistent with those from MO calculations. The molecular structure of ethynylbenzene reported from microwave spectroscopy studies is shown to be inaccurate in the ipso region of the benzene ring. The variations of the ring C-C bonds and C-C-C angles in p-diethynylbenzene and s-triethynylbenzene are well interpreted as arising from the superposition of independent effects from each substituent. In particular, experiments and calculations consistently show that the mean length of the ring C-C bonds increases by about 0.002 A per ethynyl group. MO calculations at different levels of theory indicate that though the length of the C[triple bond]C bond of the ethynyl group is unaffected by the pattern of substitution, the C(ipso)-C(ethynyl) bonds in p-diethynylbenzene are 0.001-0.002 A shorter than the corresponding bonds in ethynylbenzene and s-triethynylbenzene. This small effect is attributed to conjugation of the two substituents through the benzene ring. Comparison of experimental and MO results shows that the differences between the lengths of the C(ipso)-C(ethynyl) and C(ipso)-C(ortho) bonds in the three molecules, 0.023-0.027 A, are correctly computed at the MP2 and B3LYP levels of theory but are overestimated by a factor of 2 when calculated at the HF level.