Glycine Dimers: Structure,Stability, and Medium Effects

We report a study on different ionization states and conformations of the bimolecular (Gly)₂ system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug‐cc‐pVTZ and B3LYP/6‐311+G(2df,2p) methods on B3LYP/6‐31+G(d,p) optimized structures (some single‐point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion–zwitterion or neutral–zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (?4 kcal mol^?1). Thus, according to our results, zwitterion–zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α‐glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion–zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.     

Highly stable self-assembly in water: ion pair driven dimerization of a guanidiniocarbonyl pyrrole carboxylate zwitterion

The synthesis of a novel water-soluble guanidiniocarbonyl pyrrole carboxylate zwitterion 2 is described, and its self-association in aqueous solutions is studied. Zwitterion 2 forms extremely stable 1:1 dimers which are held together by an extensive hydrogen bonding network in combination with two mutual interacting ion pairs as could be shown by ESI MS and X-ray structure determination. NMR dilution studies in different highly polar solvents showed that dimerization is fast on the NMR time scale with association constants ranging from an estimated 10(10) M(-1) in DMSO to a surprisingly high 170 M(-1) in water. Hence, zwitterion 2 belongs to the most efficient self-assembling systems solely on the basis of electrostatic interactions reported so far. Furthermore, an amidopyridine pyrrole carboxylic acid 10 was developed as a neutral analogue of zwitterion 2, which also dimerizes with an essentially identical hydrogen bonding pattern (according to ESI MS and X-ray structure determination) but lacking the ionic interactions. NMR binding studies demonstrated that the solely hydrogen-bonded neutral dimer of 10 is stable only in organic solvents of low polarity (K > 10(4) M(-1) in CDCl3 but <10 M(-1) in 5% DMSO in CDCl3). The comparison of both systems impressively underlines the importance of ion pair interactions for stable self-association of such H-bonded binding motifs in water.     

Two New Daphniphyllum Alkaloids from Daphniphyllum calycinum

Two new daphniphyllum alkaloids named 2‐hydroxyyunnandaphnine D ( 1 ) and methyl 7‐hydroxyhomodaphniphyllate ( 2 ), together with eight known alkaloids, daphnioldhanin D, calyciphylline F, calyciphylline B, deoxycalyciphylline B, daphnicyclidin H, macropodumine C, 9,10‐epoxycalycine A, and yunnandaphnine A, were isolated from the stems and leaves of Daphniphyllum calycinum. Their structures and relative configurations were established on the basis of spectral evidence (including 2D‐NMR) and subsequently confirmed by a single‐crystal X‐ray crystallographic diffraction analysis.     

Molecular dynamics simulation of glycine zwitterion in aqueous solution

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.     

Zwitterionic Salts from the Reaction of Symmetrical and Unsymmetrical (thio)Barbituric Acids with 2‐Pyridinecarbaldehyde under Solvent‐free Condition

A simple and efficient synthesis for the preparation of unusual charge‐separated pyridinium (thio)barbiturate zwitterion derivatives was achieved via a one‐pot reaction of (thio)barbituric acid derivatives and 2‐pyridinecarbaldehyde under solvent‐free condition and also in methanol under refluxing. The structure of the compounds was confirmed by ¹H NMR, ¹³C NMR, FT‐IR, mass and X‐ray analysis. The mechanism of the formation is discussed. Instead, no related pyridinium zwitterion was afforded from the reaction between dimedone and 2‐pyridinecarbaldehyde under the same conditions and its xanthene derivative was obtained.     

Electronic spectra of benzimidazolecarboxylic acids: effect of solvents and acid concentrations

Effect of solvents and acid concentration on the absorption and fluorescence spectra of benzimidazole-2-acetic acid (BIAA), benzimidazole-2-methylacetate (BIAE) and benzimidazole-2-propionic acid have been investigated. The results have indicated that the presence of the methylene group reduces the interaction of BI and −COOH groups. For example, the spectral characteristics of BIAE and BIPA are similar to 2-methylbenzimidazole (MBI). The long wavelength absorption band in BIAA is assigned to the presence of an intramolecular hydrogen-bonded structure and hydrogen bonding is stronger in the S₁ state than in the S₀ state. In aqueous medium, depending upon the pH of the solution, BIAA and BIPA either exist as zwitterion or monoanion. The zwitterion and monoanion of BIAA have a ring structure, whereas those of BIPA have an open structure.     

A computational study on the structures of methylamine-carbon dioxide-water clusters: evidence for the barrier free formation of the methylcarbamic acid zwitterion (CH3NH2+COO-) in interstellar water ices

We investigated theoretically the interaction between methylamine (CH(3)NH(2)) and carbon dioxide (CO(2)) in the presence of water (H(2)O) molecules thus simulating the geometries of various methylamine-carbon dioxide complexes (CH(3)NH(2)/CO(2)) relevant to the chemical processing of icy grains in the interstellar medium (ISM). Two approaches were followed. In the amorphous water phase approach, structures of methylamine-carbon dioxide-water [CH(3)NH(2)/CO(2)/(H(2)O)(n)] clusters (n = 0-20) were studied using density functional theory (DFT). In the crystalline water approach, we simulated methylamine and carbon dioxide interactions on a fragment of the crystalline water ice surface in the presence of additional water molecules in the CH(3)NH(2)/CO(2) environment using DFT and effective fragment potentials (EFP). Both the geometry optimization and vibrational frequency analysis results obtained from these two approaches suggested that the surrounding water molecules which form hydrogen bonds with the CH(3)NH(2)/CO(2) complex draw the carbon dioxide closer to the methylamine. This enables, when two or more water molecules are present, an electron transfer from methylamine to carbon dioxide to form the methylcarbamic acid zwitterion, CH(3)NH(2)(+)CO(2)(-), in which the carbon dioxide is bent. Our calculations show that the zwitterion is formed without involving any electronic excitation on the ground state surface; this structure is only stable in the presence of water, i.e. in a methyl amine-carbon dioxide-water ice. Notably, in the vibrational frequency calculations on the methylcarbamic acid zwitterion and two water molecules we find the carbon dioxide asymmetric stretch is drastically red shifted by 435 cm(-1) to 1989 cm(-1) and the carbon dioxide symmetric stretch becomes strongly infrared active. We discuss how the methylcarbamic acid zwitterion CH(3)NH(2)(+)CO(2)(-) might be experimentally and astronomically identified by its asymmetric CO(2) stretching mode using infrared spectroscopy.     

"Knock-out" analogues as a tool to quantify supramolecular processes: a theoretical study of molecular interactions in guanidiniocarbonyl pyrrole carboxylate dimers

It was recently shown experimentally that 5-(guanidiniocarbonyl)-1H-pyrrole-2-carboxylate 1, a self-complementary zwitterion, dimerizes even in water with an unprecedented high association constant of K = 170 M(-1) (J. Am. Chem. Soc. 2003, 125, 452-459). To get an insight into the importance of the various noncovalent binding interactions and of their interplay (electrostatic interactions, hydrogen binding, cooperative effects), we employ density functional theory to study the stability of several "knock-out" analogues in which single hydrogen bonds within these multiple point binding motif are switched off by replacing N-H hydrogen-donor groups with either methylene groups or an oxygen ether bridge. The influence of a highly polar solvent on the dimer stabilities is also examined. These calculations reproduce the experimental data for zwitterion 1. A comparison of 1 with the arginine dimer shows that the energy contents of the monomers also significantly influence the dimer stabilities. The analysis of the various "knock-out" analogues reveals as a main conclusion that simple models either based just on hydrogen-bond counting or on the assumption that the charge interaction by itself is the main and dominant factor fail to explain the stability of such self-assembled dimers. Our computations show that the hydrogen-bond network, the electrostatic attraction, and also their mutual interactions are responsible for the high stability of zwitterion 1.     

Gas-phase zwitterion stabilization by a metal dication

Although solution-phase amino acids normally exist as zwitterions, this is not the case under gas-phase conditions, where the canonical structure is favored. Complexation to a metal ion can increase the relative zwitterion stability, but even then, the zwitterion (salt bridge, SB) form is not the most stable form of such singly charged complexes except for basic amino acids. Computation suggests enhanced SB stability for doubly charged complexes of weakly binding metal ions, but this has not hitherto been verified experimentally. Using infrared-spectroscopic characterization of the ion structure by multiple-photon infrared dissociation by the FELIX free electron laser, the Ba2+ complex of Trp has been shown to have the SB structure, and the presence of the nonzwitterionic (charge-solvated) form has been ruled out. The principal spectroscopic signatures of the SB structure are the appearance of the antisymmetric CO stretch of the carboxylate group at 1600 cm-1 and the umbrella mode of NH3 at 1400 cm-1.     

Fluorescence of cis-1-amino-2-(3-indolyl)cyclohexane-1-carboxylic acid: a single tryptophan chi(1) rotamer model

A constrained derivative, cis-1-amino-2-(3-indolyl)cyclohexane-1-carboxylic acid, cis-W3, was designed to test the rotamer model of tryptophan photophysics. The conformational constraint enforces a single chi(1) conformation, analogous to the chi(1) = 60 degrees rotamer of tryptophan. The side-chain torsion angles in the X-ray structure of cis-W3 were chi(1) = 58.5 degrees and chi(2) = -88.7 degrees. Molecular mechanics calculations suggested two chi(2) rotamers for cis-W3 in solution, -100 degrees and 80 degrees, analogous to the chi(2) = +/-90 degrees rotamers of tryptophan. The fluorescence decay of the cis-W3 zwitterion was biexponential with lifetimes of 3.1 and 0.3 ns at 25 degrees C. The relative amplitudes of the lifetime components match the chi(2) rotamer populations predicted by molecular mechanics. The longer lifetime represents the major chi(2) = -100 degrees rotamer. The shorter lifetime represents the minor chi(2) = 80 degrees rotamer having the ammonium group closer to C4 of the indole ring (labeled C5 in the cis-W3 X-ray structure). Intramolecular excited-state proton transfer occurs at indole C4 in the tryptophan zwitterion (Saito, I.; Sugiyama, H.; Yamamoto, A.; Muramatsu, S.; Matsuura,T. J. Am. Chem. Soc. 1984, 106, 4286-4287). Photochemical isotope exchange experiments showed that H-D exchange occurs exclusively at C5 in the cis-W3 zwitterion, consistent with the presence of the chi(2) = 80 degrees rotamer in solution. The rates of two nonradiative processes, excited-state proton and electron transfer, were measured for individual chi(2) rotamers. The excited-state proton-transfer rate was determined from H-D exchange and fluorescence lifetime data. The excited-state electron-transfer rate was determined from the temperature dependence of the fluorescence lifetime. The major quenching process in the -100 degrees rotamer is electron transfer from the excited indole to carboxylate. Electron transfer also occurs in the 80 degrees rotamer, but the major quenching process is intramolecular proton transfer. Both quenching processes are suppressed by deprotonation of the amino group. The results for cis-W3 provide compelling evidence that the complex fluorescence decay of the tryptophan zwitterion originates in ground-state heterogeneity with the different lifetimes primarily reflecting different intramolecular excited-state proton- and electron-transfer rates in various rotamers.     

Studies on photophysics and photochemistry of N-salicylidene-p-(N,N-dimethylamino)aniline

The fluorescence spectra of N-salicylidene-p-(N,N-dimethylamino)aniline have been investigated in various solvents and three kinds of fluorescence were found; they were that of excited intermediate, exciplex and excited dimer. According to the transient absorption spectra and decay kinetic data of photoproducts of the title compound, it has been found that the photoproducts in cyclohexane are a zwitterion and a mixed dimer formed by a zwitterion and an enol; in acetonitrile the photoproducts are a zwitterion, a mixed dimer formed by a zwitterion and an enol and a dimer formed of zwitterion. Photochromic and luminescence mechanisms of the title compound are discussed as well.     

Novel guanidinium zwitterion and derived ionic liquids: physicochemical properties and DFT theoretical studies

A new zwitterion containing 1,1,3,3-tetramethylguanidine was synthesized using a simple method, and the physicochemical properties as well as the crystal structure of the compound were also studied. Two new acidic ionic liquids (ILs) were synthesized using the zwitterion as the precursor and the physicochemical properties including density, viscosity, thermal property, and acidic scale of the ILs were investigated. A density functional theory investigation of the geometrical structures and electronic properties of the guanidinium triflate ionic liquid was also presented for better understanding the new ILs.     

Reactions of 1,1-bis(dimethylamino)-1,3-butadiene with olefins – (4 + 2) cycloadditions and zwitterion formation

1,1-Bis(dimethylamino)-1,3-butadiene ( 1 ) as a strong donor diene (E_1/2 = 0.03 V vs. SCE, 1st IP_v = 6.94 eV) is treated with acrylonitrile, dimethyl dicyanofumarate, and tetracyanoethylene. Cycloaddition with acrylonitrile is slow and requires elevated temperatures at which elimination of dimethylamine with formation of 1-cyano-2-(dimethylamino)-1,3-cyclohexadiene occurs. The reaction of 1 with TCNE at −40°C in acetonitrile is very fast and leads to the zwitterion 5 . At T ⩾ −20°C, 5 eliminates hydrogen cyanide to give a highly colored (λ_max = 489 nm, lgϵ = 4.716) merocyanine. A zwitterion 9 generated from 1 and dimethyl dicyanofumarate can be isolated in crystalline form. The structural analysis shows that the zwitterions are produced by attack of the olefin at the antiperiplanar conformation of 1 . Both zwitterions which can be trapped as crystalline picrates cannot be converted to cycloadducts. These results suggest that cycloaddition is observed if zwitterion formation becomes energetically unfavorable.     

Density functional theory study on the –SO3H functionalized acidic ionic liquids

In this work, the structures of the –SO₃H functionalized acidic ionic liquid 1-(3-sulfonic acid) propyl-3-methylimidazolium hydrogen sulfate ([C₃SO₃Hmim]HSO₄), including its precursor compound (zwitterion), cation, and cation–anion ion-pairs, were optimized systematically by the DFT theory at B3LYP/6-311++G** level, and their most stable geometries were obtained. The calculation results indicated that a great tendency to form strong intramolecular hydrogen bonds was present in the zwitterion, and this tendency was weakened in the cation that was the protonation product of zwitterion. The intramolecular hydrogen bonds and intermolecular hydrogen bonds coexisted in the ionic liquid, and they played an important role in the stability of the systems. The strongest interaction in the ionic liquid was found between the anion and the functional group. The transition state research and the intrinsic reaction coordinate analysis of the hydrogen transfer reaction showed that, when the cation and the anion interacted near the functional group by double O–H···O hydrogen bonds, the ionic liquid was inclined to exist in a form of the zwitterion and H₂SO₄.     

Bonding modes of stanna-closo-dodecaborate: eta1(Sn) to eta3(BH) rearrangement reactions in zwitterionic stanna-closo-dodecaborate ruthenium complexes

Reaction of the stanna-closo-dodecaborate salt [Bu3MeN]2[SnB11H11] with the dimeric ruthenium complex [Ru2(mu-Cl)3(triphos)2]Cl (triphos = {MeC(CH2PPh2)3}) in refluxing acetonitrile yields the zwitterionic compound [Ru(SnB11H11)(MeCN)2(triphos)] (4) which has been characterized by single-crystal X-ray diffraction analysis and solid-state NMR spectroscopy. Refluxing the zwitterion in acetone leads to an eta1(Sn) to eta3(BH) rearrangement with formation of [Ru(SnB1)H11)(triphos)] (5) whose structure has been confirmed by X-ray diffraction and multinuclear NMR spectroscopy in solution and in the solid state. Furthermore, two isomeric zwitterions fac- and mer-[Ru(SnB11H11)(dppb)(MeCN)3] (6a, 6b) and their rearrangement reactions as well as their NMR properties are described.     

Low-melting zwitterion: effect of oxyethylene units on thermal properties and conductivity

An imidazolium-based zwitterion containing two oxyethylene units was obtained as a colorless liquid at room temperature. The equimolar mixture of the liquid zwitterion and lithium bis(trifluoromethylsulfonyl)amide showed an ionic conductivity of over 10(-4) S cm(-1) at 80 °C, which was higher than those of mixtures composed of analogous solid zwitterions.     

Synthesis,crystal, and molecular structures of HIDA and its monomethyl ester

A simple procedure for synthesis of HIDA (2,6-dimethylphenylcarbamoylmethyl iminodiacetic acid) is described. It was obtained in better yield by reaction of 2,6-dimethylphenylcarbamoylmethyl chloride with iminodiacetic acid in carbon tetrachloride. The HIDA (A) was identified by IR and¹H NMR spectroscopy. Two types of crystals were detected in the crystal final product. Since they could be separated, the crystals:A andB were investigated by X-ray analysis. Crystal and molecular structures were solved by direct methods and refined by full-matrix least-squares technique toR=0.047 andR=0.056, respectively. In the structure ofA, the N2 atom is protonated and the molecule exists as a zwitterion. The crystal structure of compoundA is stabilized by strong hydrogen bonds, which are reflected in higher close-packing coefficient, density, and melting point, compared to compoundB. CompoundB is a monomethyl ester of HIDA, which is present as an impurity in the final recrystallized product.     

Kinetic Studies of the Ring-Opening Polymerization of 1-β-Cyanoethylazetidine

The ring-opening polymerization rate of 1-β-cyanoethylazetidine (CA) with 3-hydroxy-1-propanesulfonic acid sultone (HPSS) as an initiator has been investigated in acetonitrile. The polymerization of CA with HPSS proceeded by way of a zwitterion formed by the addition reaction of CA and HPSS. The course of polymerization involved, as an early stage, slow initiation due to the low reactivity of the zwitterion. The propagation constants were obtained as were the enthalpy of activation for propagation (ΔH_p? = 12 kcal/mol) and the entropy of activation for propagation (ΔS_p? = ?31 cal/K·mol).     

Ionization and Partitioning Profiles of Zwitterions: The case of the anti-inflammatory drug azapropazone

Azapropazone ( 1 ) is a non-steroidal anti-inflammatory drug (NSAID) whose chemical structure is markedly different from that of other agents in this class and challenges our understanding of structure-activity and structure-permeation relationships. Using a variety of experimental and computational techniques, we studied 1 for its molecular structure in the gas phase and non-protic polar solvents, protonation/deprotonation equilibra, tautomerism, and pH-lipophilicity profiles (octan-1-ol/H₂O and dodecane/H₂O). Other NSAIDs and model compounds were also examined for comparison. Due to its very low acidic pK_a1, 1 exists in the physiological pH range as a zwitterion and as an anion. Some pharmacological implications of these findings are discussed.     

Biradical processes in reactions between benzyne and tropone

The title reactions were investigated experimentally and theoretically. The benzyne--tropone pair has been known to give a Diels?CAlder [4+2] cycloadduct. However, in the present experiment using two sources of benzyne, many unexpected products were obtained. In particular, a zwitterion with a C?CCl bond is strikingly a major product, the structure of which was determined by the X-ray analysis. The bond is formed by quenching the Cl atom from the solvent CH₂Cl₂, which demonstrates that the reactions proceed via radical processes. DFT calculations revealed the elementary processes of the reactions. The presence of the novel zwitterion in the solid state has been interpreted in terms of the permanent dipole?Cdipole attractions/interactions/stabilization.