Theoretical analysis of pyridine protonation in water clusters of increasing size.

The protonation of pyridine in water clusters as a function of the number of water molecules was theoretically analyzed as a prototypical case for the protonation of organic bases. We determined the variation of structural, bonding, and energetic properties on protonation, as well as the stabilization of the ionic species formed. Thus, we used supermolecular models in which pyridine interacts with clusters of up to five water molecules. For each complex, we determined the most stable unprotonated and protonated structures from a simulated annealing at the semi ab initio level. The structures were optimized at the B3LYP/cc-pVDZ level. We found that the hydroxyl group formed on protonation of pyridine abstracts a proton from the ortho-carbon atom of the pyridine ring. The "atoms in molecules" theory showed that this C-H group loses its covalent character. However, starting with clusters of four water molecules, the C-H bond recovers its covalent nature. This effect is associated with the presence of more than one ring between the water molecules and pyridine. These rings stabilize, by delocalization, the negative charge on the hydroxyl oxygen atom. Considering the protonation energy, we find that the protonated forms are increasingly stabilized with increasing size of the water cluster. When zero-point energy is included, the variation follows closely an exponential decrease with increasing number of water molecules. Analysis of the vibrational modes for the strongest bands in the IR spectra of the complexes suggests that the protonation of pyridine occurs by concerted proton transfers among the different water rings in the structure. Symmetric water stretching was found to be responsible for hydrogen transfer from the water molecule to the pyridine nitrogen atom.     

The importance of tetrahedrally coordinated molecules for the explanation of liquid water properties.

Ab initio calculations on molecular clusters and a quantum statistical model are used to probe the structure of liquid water and its anomalies. Characteristic temperature dependent mixtures of ring and three-dimensional, voluminous water clusters provide the famous density maximum. The mixture model also reproduces the shift of the density maximum as a function of pressure and isotopic substitution. This finding is consistent with femtosecond spectroscopy data suggesting that two distinct molecular species exist in liquid water. The given structures also reproduce the oxygen-oxygen pair correlation function and the vibrational IR spectrum of liquid water. The results underline the importance of three-dimensional, tetrahedrally coordinated structures for the understanding of water anomalies and the existence of two liquid phases in the supercooled region.     

How Cations Change Peptide Structure

Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of either Li⁺ or Na⁺ by using state‐of‐the‐art density‐functional theory (including van der Waals effects) and gas‐phase infrared spectroscopy. These monovalent cations have a drastic effect on the local backbone conformation of turn‐forming peptides, by disruption of the hydrogen‐bonding networks, thus resulting in severe distortion of the backbone conformations. In fact, Li⁺ and Na⁺ can even have different conformational effects on the same peptide. We also assess the predictive power of current approximate density functionals for peptide–cation systems and compare to results with those of established protein force fields as well as high‐level quantum chemistry calculations (CCSD(T)).     

Theoretical and experimental study of the adsorption of neutral glycine on silica from the gas phase.

The adsorption of neutral glycine onto amorphous silica was investigated both theoretically and experimentally. DFT calculations were performed at the BLYP-631++G** level using a cluster approach. Several possible configurations involving the formation of H bonds between glycine and one, two, or three silanol groups (SiOH) were considered. The most favorable bonding of glycine with one silanol group (45 kJ mol(-1)) occurs through the COOH moiety, thus forming a cycle in which the CO group is an H-bond acceptor whereas the acidic OH group is an H-bond donor. With two or three silanol groups, additional H bonds are formed between the amine moiety and the silanol groups, which leads to an increased adsorption energy (70 and 80 kJ mol(-1) for two and three silanol groups, respectively). Calculated nu(CO), delta(HNH), and delta(HCH) values are sensitive to the adsorption mode. A bathochromic shift of nu(CO) as compared to the nu(CO) of free glycine (calculated in the 1755-1790 cm(-1) range) is found for glycine in interaction with silanol(s). The more H bonds are formed between the COOH moiety and silanol groups, the higher the bathochromic shift. For delta(HNH), no shift is found for glycine adsorbed on one and two silanol groups (where the amine is either not bound or an H-bond donor), whereas a bathochromic shift is calculated with three silanols when the amine moiety is an H-bond acceptor. Experimental FTIR spectra performed at room temperature for glycine adsorbed at 160 degrees C on Aerosil amorphous silica exhibit bands at 1371, 1423, 1630, and 1699 cm(-1). The experimental/calculated frequencies have their best correspondence for glycine adsorbed on two silanol groups. It is important to note that the forms giving the best correspondence to experimental frequencies are the most stable ones.     

Noncovalent complexes between dimethyl ether and formic acid--an ab initio and matrix isolation study.

The complexes formed by noncovalent interactions between formic acid and dimethyl ether are investigated by ab initio methods and characterized by matrix isolation spectroscopy. Six complexes with binding energies between -2.26 and -7.97 kcal mol(-1) (MP2/cc-pVTZ+zero point vibrational energy+basis set superposition erros) are identified. The two strongest bound complexes are, within a range of 0.3 kcal mol(-1), isoenergetic. The binding in these six dimers can be described in terms of OH...O, C=O...H, C-O...H and CH...O interactions. Matrix isolation spectroscopy allowed to characterize the two strongest bound complexes by their infrared spectra.     

Ion-pair formation in the ionic liquid 1-ethyl-3-methylimidazolium bis(triflyl)imide as a function of temperature and concentration.

The structures and ion-pair formation in the ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are studied by a combination of FTIR measurements and DFT calculations. We could clearly distinguish imidazolium cations that are completely H-bonded to anions from those that are single H-bonded in ion pairs. Ion-pair formation already occurs in the neat IL and rises with temperature. Ion-pair formation is strongly promoted by dilution of the IL in chloroform. In these weakly polar environments ion pairs H-bonded via C(2)H are strongly favored over those H-bonded via C(4,5)H. This finding is in agreement with DFT (gas phase) calculations, which show a preference for ion pairs H-bonded via C(2)H as a result of the acidic C(2)H bond.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

Theoretical Study on Hydrogen‐Bond Effects in IR Spectra of High‐ and Low‐Temperature Phases of Nitric Acid Dihydrate

The low‐ and high‐temperature phases (α and β, respectively) of solid nitric acid dihydrate (NAD) are studied in depth by DFT methods. Each phase contains two types of complex structures (H₃O⁺) ? (H₂O), designated A and B, with different hydrogen‐bonding (HB) characteristics. The theoretical study reveals that type A complexes are weakly bound and could be described as (H₃O)⁺ and H₂O aggregates, with decoupled vibrational modes, whereas in type B structures the proton is situated close to the centre of the O ??? O bond and induces strong vibrational coupling. The proton‐transfer mode is predicted at quite different wavenumbers in each complex, which provides an important differentiating spectral feature, together with splitting of some bands in β‐NAD. Theoretical spectra are estimated by using two GGA parameterizations, namely, PBE and BLYP. The potential‐energy surface for each type of HB in NAD is also studied, as is the spectral influence of displacement of the shared H atom along the O? O bond. The results are compared to literature infrared spectra recorded by different techniques, namely, transmission and reflection–absorption, with both normal and tilted incident radiation. This work provides a thorough assignment of the observed spectra, and predictions for some spectra not yet available. The usefulness of high‐level theoretical calculations as performed herein to discriminate between two phases of a solid crystal is thus evidenced.     

Dipeptide structure determination by vibrational circular dichroism combined with quantum chemistry calculations.

The solution structure and the local solvation environments of alanine dipeptide (AD, 1 a) and its isotopomer (AD*, 1 b, 13C on the acetyl end C==O) are studied by using infrared (IR) spectroscopy and vibrational circular dichroism (VCD). From the amide I IR spectra of AD* in various protic solvents, it is found that each of the two carbonyl groups is fully H-bonded to two water molecules. However, the number of alcohol molecules H-bonded to each C==O varies from one to two, and the local solvation environments are asymmetric around the two peptides of AD* in alcohol solutions. The amide I VCD spectra of AD and AD* in D2O are also measured, and a series of density functional theory (DFT, B3LYP/6-311++G**) calculations are performed to obtain the amide I normal-mode rotational strengths of AD and the intrinsic rotational strengths of its two peptide fragments. By combining the VCD-measurement and DFT-calculation results and employing a coupled oscillator theory, we show that the aqueous-solution structure of the dipeptide can be determined. We believe that the present method will be of use in building up a library of dipeptide solution structures in water.     

Directing Foldamer Self-Assembly with a Cyclopropanoyl Cap

The rational design of self-assembling organic materials is extremely challenging due to the difficulty in precisely predicting solid-state architectures from first principles, especially if synthons are conformationally flexible. A tractable model system to study self-assembly was constructed by appending cyclopropanoyl caps to the N termini of helical α/β-peptide foldamers, designed to form both N−H⋅⋅⋅O and C^α−H⋅⋅⋅O hydrogen bonds, which then rapidly self-assembled to form foldectures (foldamer architectures). Through a combined analytical and computational investigation, cyclopropanoyl capping was observed to markedly enhance self-assembly in recalcitrant substrates and direct the formation of a single intermolecular N−H⋅⋅⋅O/C^α−H⋅⋅⋅O bonding motif in single crystals, regardless of peptide sequence or foldamer conformation. In contrast to previous studies, foldamer constituents of single crystals and foldectures assumed different secondary structures and different molecular packing modes, despite a conserved N−H⋅⋅⋅O/C^α−H⋅⋅⋅O bonding motif. DFT calculations validated the experimental results by showing that the N−H⋅⋅⋅O/C^α−H⋅⋅⋅O interaction created by the cap was sufficiently attractive to influence self-assembly. This versatile strategy to harness secondary noncovalent interactions in the rational design of self-assembling organic materials will allow for the exploration of new substrates and speed up the development of novel applications within this increasingly important class of materials.     

Dissecting Noncovalent Interactions in Carboxyl-Functionalized Ionic Liquids Exhibiting Double and Single Hydrogens Bonds Between Ions of Like Charge

We show that the carboxyl-functionalized ionic liquid 1-(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC-CH₂-py][NTf₂] exhibits three types of hydrogen bonding: the expected single hydrogen bonds between cation and anion, and, surprisingly, single and double hydrogen bonds between the cations, despite the repulsive Coulomb forces between the ions of like charge. Combining X-ray crystallography, differential scanning calorimetry, IR spectroscopy, thermodynamic methods and DFT calculations allows the analysis and characterization of all types of hydrogen bonding present in the solid, liquid and gaseous states of the ionic liquid (IL). We find doubly hydrogen bonded cationic dimers (c⁺=c⁺) in the crystalline phase. With increasing temperature, this binding motif opens in the liquid and is replaced by (c⁺−c⁺−a⁻ species, with a remaining single cationic hydrogen bond and an additional hydrogen bond between cation and anion. We provide clear evidence that the IL evaporates as hydrogen-bonded ion pairs (c⁺−a⁻) into the gas phase. The measured transition enthalpies allow the noncovalent interactions to be dissected and the hydrogen bond strength between ions of like charge to be determined.