Unprotonated Nitrogen Research Articles

Porphyrins on acid: kinetics of the photoinduced-protonation of tetrakis(4-carboxyphenyl)-porphyrin.

Free-base porphyrins can be protonated, which significantly impacts their electronic and excited state properties. While excited state dynamics are well explored for either neutral or fully protonated porphyrins, the intermediate region has not yet been explored, although their potential implications for photocatalytic reactions are evident. This study explores how partial protonation affects the nature and properties of photoexcited states of tetrakis(4-carboxyphenyl)porphyrin (TCPP) using steady-state and nanosecond transient absorption spectroscopy. Global-fit analysis of the decay curves revealed the formation of a protonated excited triplet state from the neutral triplet state, as well as the long lifetimes of these species of up to 120 μs. The photoexcited triplet state of TCPP functions as a photobase, which was confirmed by computational analysis of the electron density of the exited states showing increased nucleophilicity at the unprotonated nitrogen atoms of the porphyrin core. These findings indicate that photoinduced protonated excited triplet states can function as electron acceptors with anodically shifted redox potentials, opening new pathways for porphyrin-based photoreactions.

Ab initio molecular dynamics study of proton transport in imidazolium-based ionic liquids with added imidazole.

Development of efficient anhydrous proton-conducting materials would expand the operational temperature ranges of hydrogen fuels cells (HFCs) and eliminate their dependence on maintaining sufficient hydration levels to function efficiently. Protic ionic liquids (PILs), which have high ionic densities and low vapor pressures, have emerged as a potential material for proton conducting layers in HFCs. In this work, we investigate proton transport via the Grotthuss mechanism in 1-ethylimidazolium bis-(trifluoromethanesulfonyl)imide ([C2HIm][TFSI]) protic ionic liquids with added imidazole (Im0) using ab initio molecular dynamics. In particular, we vary the composition of the systems studied from pure [C2HIm][TFSI] to those where the mole fraction of Im0 is 0.67. Given the large difference in pKa between C2HIm+ and HTFSI, TFSI- does not accept acidic protons from C2HIm+; conversely, imidazolium (HIm+) and C2HIm+ have very similar pKa values, and thus Im0 can readily accept protons. We find that the unprotonated nitrogen on Im0 dominates solvation of the labile protons on C2HIm+ and other Im0 species, resulting in formation of robust imidazole wires. Given the amphoteric nature of Im0, i.e. its ability to accept and donate protons, these wires provide conduits along which protons can rapidly traverse via the Grotthuss mechanism, thereby greatly increasing the proton coefficient of self-diffusion. We find that the average length of the wires increases with added Im0, and thus as the mole fraction of Im0 increases so too does the proton diffusion constant. Lastly, we analyze our trajectories to determine the energy and time scales associated with proton transfer.

Field evidence for enhanced generation of reactive oxygen species in atmospheric aerosol containing quinoline components

Organic constituents of atmospheric particular matter (PM) contribute significantly to prompt generation of reactive oxygen species (ROS) in particle phase, which is often quantified in terms of its oxidative potential (OP). In this study, we used complementary methods of the advanced molecular characterization and the OP quantitation to explore potential of different organic species to enhance ROS generation in ambient aerosol samples. We used seven PM2.5 samples collected in the Midwest US, and extracted them sequentially into a set of solvents with different polarity: first non-polar hexane (HEX), then moderately polar dichloromethane (DCM) and finally polar deionized (DI) water. The DI extracts were further separated using solid phase extraction to isolate water-soluble organic carbon (WSOC) from inorganic ions. The OP of obtained extracts was analyzed using dithiothreitol (DTT) assay and reported here in terms of the DTT consumption rate (called DTT activity). The molecular composition of the same extracts was analyzed using a tandem platform of high-performance liquid chromatography (HPLC) coupled with a photodiode array detector (PDA) and a high-resolution mass spectrometer (HRMS). Highest DTT activities were observed in WSOC fractions (>1.1 μM min−1) followed by DCM (0.75–1.1 μM min−1) and HEX (<0.75 μM min−1) fractions, respectively. These results were complemented by the HPLC-PDA-HRMS molecular characterization data indicating numerous redox-active polar organics detected in the WSOC fractions. In particular, chemical component with elemental formula of C11H11N - attributed to dimethyl quinoline (DMQ) - was found systematically across all DTT-active fractions. The unprotonated nitrogen atom in the pyridine ring of quinolines facilitates electron transfer in the redox reactions, catalyzing generation of ROS in the quinoline containing samples. This is the first study that unambiguously identifies quinoline as a promoter of ROS generation determined within complex mixtures of ambient organic aerosols.

15N NMR Shifts of Eumelanin Building Blocks in Water: A Combined Quantum Mechanics/Statistical Mechanics Approach.

Theoretical results for the magnetic shielding of protonated and unprotonated nitrogens of eumelanin building blocks including monomers, dimers, and tetramers in gas phase and water are presented. The magnetic property in water was determined by carrying out Monte Carlo statistical mechanics sampling combined with quantum mechanics calculations based on the gauge-including atomic orbitals approach. The results show that the environment polarization can have a marked effect on nitrogen magnetic shieldings, especially for the unprotonated nitrogens. Large contrasts of the oligomerization effect on magnetic shielding show a clear distinction between eumelanin building blocks in solution, which could be detected in nuclear magnetic resonance experiments. Calculations for a -stacked structure defined by the dimer of a tetrameric building block indicate that unprotonated N atoms are significantly deshielded upon stacking, whereas protonated N atoms are slightly shielded. The results stress the interest of NMR experiments for a better understanding of the eumelanin complex structure.

Facile Supramolecular Engineering of Porphyrin cis Tautomers: The Case of β-Octabromo-meso-tetraarylporphyrins.

A porphyrin cis tautomer, where the two central NH protons are on adjacent pyrrole rings, has long been invoked as an intermediate in porphyrin tautomerism. Only recently, however, has such a species been isolated and structurally characterized. Thus, single-crystal X-ray structure determinations of two highly saddled free-base porphyrins, β-heptakis(trifluoromethyl)-meso-tetrakis(p-fluorophenyl)porphyrin, H2[(CF3)7TFPP], and β-octaiodo-5,10,15,20-tetrakis(4′-trifluoromethylphenyl)porphyrin, H2[I8TCF3PP], unambiguously revealed cis tautomeric structures, each stabilized as a termolecular complex with a pair of ROH (R = CH3 or H) molecules that form hydrogen-bonded N–H···O–H···N straps connecting the central NH groups with the antipodal unprotonated nitrogens. The unusual substitution patterns of these two porphyrins, however, have left open the question how readily such supramolecular assemblies might be engineered, which prompted us to examine the much more synthetically accessible β-octabromo-meso-tetraphenylporphyrins. Herein, single-crystal X-ray structures were obtained for two such compounds, 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4′-trifluoromethylphenyl)porphyrin, H2[Br8TCF3PP], and 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4′-fluorophenyl)porphyrin, H2[Br8TFPP], and although the central hydrogens could not all be located unambiguously, the electron density could be convincingly modeled as porphyrin cis tautomers, existing in each case as a bis-methanol adduct. In addition, a perusal of the Cambridge Structural Database suggests that there may well be additional examples of porphyrin cis tautomers that have not been recognized as such. We are therefore increasingly confident that porphyrin cis tautomers are readily accessible via supramolecular engineering, involving the simple stratagem of crystallizing a strongly saddled porphyrin from a solvent system containing an amphiprotic species such as water or an alcohol.

Electrochemical Behavior of Copper Ion Complexed with Nanoparticle Organic Hybrid Materials

Nanoscale Organic Hybrid Materials (NOHMs) have unique properties that show potential for their use as novel electrolytes that can interact with redox active species. In this work, we probe the effects of adding poly(ethyleneimine)-based NOHMs (NOHM-I-PEI) on copper ion electrochemical reactions. As NOHM-I-PEI is added to a solution containing Cu(II), the voltammetric peak current decreases. This is likely caused by strong complex formation between the PEI nitrogen and the copper, similar to complexation observed in solutions of the polymer with copper. Upon copper addition to a NOHM-I-PEI solution, the pH decreases from 10.1, plateauing at pH = 5.3 at ∼3:1 N:Cu ratio indicating that Cu(II) displaces protons. The UV–visible spectra exhibit a Cu-PEI peak, the intensity of which levels off at ∼2.8 N:Cu. Acid titration of the N-moieties of the PEI reveals three inflections corresponding to N-environments in the PEI. Upon controlling the pH of the solution by buffering, the “sequestration” of Cu(II) is found to occur when there are unprotonated nitrogens present in the NOHM-I-PEI system; this phenomenon is also supported by UV-vis results. This work highlights the potential of and the design of NOHMs to carry charged electroactive species in solutions along with key factors to control for optimal function.

On the calculation of magnetic properties of nucleic acids in liquid water with the sequential QM/MM method

We present calculations of nuclear magnetic shieldings of the nucleic acids adenine, cytosine, guanine e thymine in liquid water environment in normal thermodynamic condition. The study is based on a sequential approach, where a classical Monte Carlo simulation of the solvated system is performed to generate the different solute–solvent configurations to be used in the following quantum mechanics calculations of magnetic properties. We find that the environment polarization effect shields the unprotonated nitrogens, with solvent shifts for the magnetic shieldings between +10.52 and +48.95 ppm. Protonated and amino nitrogens are less shielded by amounts of −17.77 and +0.22 ppm. The results obtained from supermolecule calculations show that protonated and amino nitrogen magnetic shieldings are particularly sensitive to the hydrogen bond interactions, with solvent shifts between −5.48 and −33.42 ppm, when the first microsolvation shell is explicitly considered. In addition, the supermolecular calculations also show a marked deshielding effect for the hydrogens of the protonated nitrogens, with solvent shifts between −2.43 and −5.12 ppm. There is an overall agreement between the theoretical predictions for the 1H and 15N chemical shifts and the available experimental results.

Molecular Structure of a Free-Base β-Octaiodo-meso-tetraarylporphyrin. A Rational Route tocisPorphyrin Tautomers?

Although a cis tautomer has long been invoked as an intermediate in porphyrin tautomerism, the first such species was only recently isolated and structurally characterized in the form of a β-heptakis(trifluoromethyl)-meso-tetraarylporphyrin. Reported herein is the molecular structure of a β-octaiodo-meso-tetraarylporphyrin solvate, which also exhibits a cis tautomeric structure. Both structures implicate two factors as critical to the stabilization of the cis tautomeric form—a free-base porphyrin that is naturally strongly saddled on steric grounds and a hydroxylic or amphiprotic solvent that can provide hydrogen-bonded N–H···X-H···N (X = O in both the above examples) straps connecting the central NH groups with the antipodal unprotonated nitrogens. The results raise the prospect that a rational strategy affording cis porphyrin tautomers in a predictable manner may be within reach.

Insights on the interaction of Zn2 + cation with triazoles: Structures, bonding, electronic excitation and applications

At present, we investigate the structures, the stability, the bonding and the spectroscopy of the Zn2+-triazole complexes (Zn2+-Tz), which are subunits of triazolate based porous materials and Zn-enzymes. This theoretical work is performed using ab initio methods and density functional theory (DFT) where dispersion correction is included. Through these benchmarks, we establish the ability and reliability of M05-2X+D3 and PBE0+D3 functionals for the correct description of Zn2+-Tz bond since these DFTs lead to close agreement with post Hartree-Fock methods. Therefore, M05-2X+D3 and PBE0+D3 functionals are recommended for the characterization of larger organometallic complexes formed by Zn and N-rich linkers. For Zn2+-Tz, we found two stable σ-type complexes: (i) a planar structure where Zn2+ links to unprotonated nitrogen and (ii) an out-of-plane cluster where carbon interacts with Zn2+. The most stable isomers consist on a coordinated covalent bond between the lone pair of unprotonated nitrogen and the vacant 4s orbital of Zn2+. The roles of covalent interactions within these complexes are discussed after vibrational, NBO, NPA charges and orbital analyses. The bonding is dominated by charge transfer from Zn2+ to Tz and intramolecular charge transfer, which plays a vital role for the catalytic activity of these complexes. These findings are important to understand, at the microscopic level, the structure and the bonding within triazolate based macromolecular porous materials and Zn-enzymes.

Double cross polarization for the indirect detection of nitrogen-14 nuclei in magic angle spinning NMR spectroscopy.

Nitrogen-14 NMR spectra at fast magic-angle spinning rates can be acquired indirectly by means of two-dimensional techniques based on double cross polarization transfer 1H → 14N →1H. Experimental evidence is given for polycrystalline samples of glycine, l-histidine, and the dipeptide Ala-Gly. Either one-bond or long-range correlations can be favored by choosing the length of the cross polarization contact pulses. Longer contact pulses allow the detection of unprotonated nitrogen sites. In contrast to earlier methods that exploited second-order quadrupolar/dipolar cross-terms, cross polarization operates in the manner of the method of Hartmann and Hahn, even for 14N quadrupolar couplings up to 4 MHz. Simulations explain why amorphous samples tend to give rise to featureless spectra because the 14N quadrupolar interactions may vary dramatically with the lattice environment. The experiments are straightforward to set up and are shown to be effective for different nitrogen environments and robust with respect to the rf-field strengths and to the 14N carrier frequency during cross polarization. The efficiency of indirect detection of 14N nuclei by double cross polarization is shown to be similar to that of isotopically enriched 13C nuclei.

Stability of van der Waals complexes of the greenhouse effect gases NH3, SO2 and CO with imidazole in gas mixtures containing CO2

The NH3, SO2 and CO van der Waals complexes with imidazole are characterized using highly correlated ab initio methods. The aim is to compare the behavior of greenhouse effect gases and pollutants in the presence of imidazole for predicting the ability of new materials, such as Zeolite Imidazolate Frameworks (ZIF’s), for CO2 capture, storage and gas filters. Imidazole is considered as the simplest model to study the nature of host-guest interactions in ZIF’s.Hydrogen bonding plays an important role in these polar gas capture processes, leading to three equilibrium structures of the imidazole+NH3, five of the imidazole+SO2, and twelve of the imidazole+CO. Real harmonic frequencies confirm the minimum energy character of these geometries. The complexation processes carry out important changes in the charge distribution of the ring. Binding energies calculated with CCSD(T)-F12 theory predict a favored adsorption of ammonia with respect to CO2. In this case, the formation of intramolecular bonds involving the unprotonated nitrogen is clearly favored energetically. The binding energy corresponding to the most stable structure I1A of SO2 is approximately twice of the corresponding value of CO2. Carbon monoxide presents the largest number of possible equilibrium structures which assure its capture by solid ZIF’s although binding energies are relatively low.

Growth and characterization of l-histidinium – 4-nitrobenzoate (1:1) multi-component molecular complex

A novel phase by reaction of l-histidine with 4-nitrobenzoic acid (4NBA) was obtained by solvent assisted grinding (SAG). The complex was crystallized from aqueous solution and characterized by X-ray powder diffraction (XRPD), single-crystal X-ray diffraction (SCXRD), infrared spectroscopy (FTIR) and thermal analysis (DSC/TGA). Additionally, the non-linear optical (NLO) properties were assessed for second harmonic generation (SHG). XRPD confirmed that a new phase was obtained, and this can be obtained pure from solution. However, when the complex appeared in SAG experiments, it was always in equilibrium with the precursors. The crystal structure of the complex revealed that a proton transfer took place from the carboxylic acid group of 4NBA to the unprotonated nitrogen atom in the imidazole ring of l-histidine to yield l-histidinium – 4-nitrobenzoate (LH4NBE) molecular complex. The FTIR spectroscopy depicted accurately the molecular characteristics of LH4NBE and the thermal analysis showed that it is stable up to 190 °C. Unfortunately, the complex displayed poor NLO properties and the sample suffered damage upon laser excitation.

Proton Transfer, Hydrogen Bonding, and Disorder: Nitrogen Near-Edge X-ray Absorption Fine Structure and X-ray Photoelectron Spectroscopy of Bipyridine–Acid Salts and Co-crystals

The sensitivity of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to Bronsted donation and the protonation state of nitrogen in the solid state is investigated through a series of multicomponent bipyridine–acid systems alongside X-ray photoelectron spectroscopy (XPS) data. A large shift to high energy occurs for the 1s → 1π* resonance in the nitrogen K-edge NEXAFS with proton transfer from the acid to the bipyridine base molecule and allows assignment as a salt (C═NH+), with the peak ratio providing the stoichiometry of the types of nitrogen species present. A corresponding binding energy shift for C═NH+ is observed in the nitrogen XPS, clearly identifying protonation and formation of a salt. The similar magnitude shifts observed with both techniques relative to the unprotonated nitrogen of co-crystals (C═N) suggest that the chemical state (initial-state) effects dominate. Results from both techniques reveal the sensitivity to identify proton transfer, hydrogen bond disorder, and even the...

Effect of Cation on Proton Conductivity of a Non-fluorinated Ionic Liquid

1-Ethyl-3-methyl imidazolium hydrogensulfate (EMIHSO4), a non-fluorinated IL, was studied both as liquid and polymer electrolytes for electrochemical capacitors [1]. While EMIHSO4exhibited a reasonable ionic conductivity, improvement in proton conductivity is possible by altering the structure of the cation, which warrants further investigation. The objectives of this study are twofold: to investigate the effect of cationic functional groups on the properties of the IL; and to select and characterize the IL system with optimum proton conductivity. The electrolytes were prepared using ILs with different cations, namely 1-ethyl-3-methyl imidazolium hydrogensulfate (EMIHSO4), 1-methylimidazolium hydrogensulfate (MIHSO4), and imidazolium hydrogensulfate (ImHSO4) in methanol solutions. For comparison, a solution of EMIHSO4 with propylene carbonate (PC), an aprotic solvent, was prepared with the same concentration as those in methanol-based electrolytes. To demonstrate the proton conductivity of the electrolytes, standard two-electrode cells were assembled utilizing pseudocapacitive electrodes such as RuO2and nanocarbon/polyoxometalate (POMs) composites [2].The cell performance were characterized using cyclic voltammtery (CV) and ac impedance spectroscopy. RuO2 exhibits pseudocapacitance via a coupled proton–electron transfer in a protic electrolyte. Figure 1 shows the CV profiles of the RuO2-based cells in all electrolytes. The ImHSO4 and MIHSO4-based cells demonstrated similar CVs and the highest capacitance performance. Their higher capacitance compared to EMIHSO4-based cell indicates the higher proton conductivity of ImHSO4 and MIHSO4, which can contribute to the electrochemical reactions of RuO2 electrodes. Due to the role of solvent on proton dissociation, the cell performance was superior using EMIHSO4/MeOH electrolytes than that for EMIHSO4/PC. The proton conductivity of PILs was further examined on a carbon/POM electrode and compared to the bare carbon electrodes. POMs involve fast and reversible multielectron transfer reactions in proton containing electrolytes. For a better comparison, the respective carbon/POM cells were also tested in 0.5M H2SO4. The electrochemical performance of the carbon/POM-based cells in the PIL electrolytes followed a similar trend as those for RuO2-based electrolytes. Figure 2 (a) shows the CV profiles of the carbon/POM-based cells and the bare carbon in ImHSO4/MeOH electrolyte. The increased capacitance of the carbon/POM cell over that for the bare carbon implies the proton conducting characteristic of ImHSO4 electrolyte which participates in the redox reaction of the POM. Figure 2 (b) presents the capacitance ratio of the carbon/POM cells in the respective PILs to H2SO4 electrolyte. ImHSO4-based cells showed the highest capacitance ratio followed by MIHSO4 and EMIHSO4in both MeOH and PC solutions. Imidazoles consist of two nitrogen sites, and their protonated and unprotonated nitrogen functions may act as proton donor and acceptor in proton transfer reactions. As the nitrogen sites decrease in MI and EMI cations, the contribution from proton conduction becomes smaller. More details on optimizing the proton conductivity of these PILs for room temperature applications, especially polymer electrolytes will be presented.

Mycobacterium tuberculosis DNA gyrase ATPase domain structures suggest a dissociative mechanism that explains how ATP hydrolysis is coupled to domain motion

DNA gyrase, a type II topoisomerase, regulates DNA topology by creating a double-stranded break in one DNA duplex and transporting another DNA duplex [T-DNA (transported DNA)] through this break. The ATPase domains dimerize, in the presence of ATP, to trap the T-DNA segment. Hydrolysis of only one of the two ATPs, and release of the resulting Pi, is rate-limiting in DNA strand passage. A long unresolved puzzle is how the non-hydrolysable ATP analogue AMP-PNP (adenosine 5'-[β,γ-imido]triphosphate) can catalyse one round of DNA strand passage without Pi release. In the present paper we discuss two crystal structures of the Mycobacterium tuberculosis DNA gyrase ATPase domain: one complexed with AMP-PCP (adenosine 5'-[β,γ-methylene]triphosphate) was unexpectedly monomeric, the other, an AMP-PNP complex, crystallized as a dimer. In the AMP-PNP structure, the unprotonated nitrogen (P-N=P imino) accepts hydrogen bonds from a well-ordered 'ATP lid', which is known to be required for dimerization. The equivalent CH2 group, in AMP-PCP, cannot accept hydrogen bonds, leaving the 'ATP lid' region disordered. Further analysis suggested that AMP-PNP can be converted from the imino (P-N=P) form into the imido form (P-NH-P) during the catalytic cycle. A main-chain NH is proposed to move to either protonate AMP-P-N=P to AMP-P-NH-P, or to protonate ATP to initiate ATP hydrolysis. This suggests a novel dissociative mechanism for ATP hydrolysis that could be applicable not only to GHKL phosphotransferases, but also to unrelated ATPases and GTPases such as Ras. On the basis of the domain orientation in our AMP-PCP structure we propose a mechanochemical scheme to explain how ATP hydrolysis is coupled to domain motion.

Protonation state of core nitrogens in the meso-tetra(4-carboxyphenyl)porphyrin impacts the chemical and physical properties of nanostructures formed in acid solutions

Organic self-assemblies of meso-tetra (4-carboxyphenyl)porphine (TCPP) prepared in trifluoroacetic acid (TFA) and hydrochloric acid solutions at pH &lt; 1 were studied by X-ray photoelectron spectroscopy (XPS) in order to determine the protonation state of the porphyrin building blocks present in the solid self-assembled nanostructures. XPS measurements were conducted both at room and at elevated temperatures. Room temperature N 1s spectra showed two bands with a 3:1 intensity ratio consistent with three protonated and one unprotonated nitrogen in the structures prepared in both TFA and HCl solutions. We attribute this result to TCPP existing as a 50:50 mixture of the free-base and diacid forms of the porphyrin core in the self-assembled state. Upon heating to 150 °C the TCPP/TFA and TCPP/HCl nanomaterials exhibit loss of pyrrolic hydrogens and retain different amounts of their respective counter ions. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of the nanostructures showed that these systems have different morphologies depending on the acid employed during fabrication and the post preparation temperature treatment. High resolution transmission electron microscopy (HRTEM) and selected area electron diffraction (SAED) of the TCPP nanostructures indicate that those prepared in HCl are crystalline while the nanoassemblies made in TFA are polycrystalline or amorphous.

Development of a polyaniline nanofiber-based carbon monoxide sensor for hydrogen fuel cell application

The sensing of carbon monoxide (CO) impurity contained in hydrogen fuel is a challenging work in the field of low temperature proton exchange membrane fuel cell (PEMFC). In the present work a chemiresistive gas sensor based on polyaniline (PANI) nanofibers was developed to detect CO in hydrogen. The sensor was fabricated by a template-free electrochemical polymerization of aniline on an interdigitated electrode. The most distinctive feature of the fabricated sensor was the formation of a horizontally oriented, monolayered PANI nanofiber network on the insulating gap area. The gas sensing character of the PANI nanosensor was evaluated by measuring the change in electrical resistance when gas atmosphere was changed from pure hydrogen to mixtures of CO in hydrogen. The results demonstrated that the PANI nanosensor had an excellent responding ability on CO in hydrogen with a concentration as low as 1 ppm. The influences of parameters, such as nanostructure, doping level, dopants, and CO concentrations, on the sensing characters of the nanosensor were discussed. The responding mechanism was attributed to the different binding sites of CO and H2 with PANI: H2 with the protonated amine nitrogen atoms and CO with the unprotonated amine nitrogen atoms. In view of its novel sensing mechanism and high sensing performance, the fabricated sensor is very promising to be applied as a new type of CO sensor to prevent the catalysis poisoning of PEMFC.

Computational study of aza-adamantanes as multivalent bases

Structure and bonding characteristics, and gas phase stepwise basicities of proposed multivalent bases 1,3,5,7-tetraazatricyclo[3.3.1.1(3,7)]decane, 1,3,5,7,9,10-hexaazatricyclo[3.3.1.1(3,7)]decane and tricyclo[3.3.1.1(3,7)]azadecane, named and abbreviated here respectively as tetra-aza-adamantane (TAA), hexa-aza-adamantane (HAA) and deca-aza-adamantane (DAA), have been studied using B3LYP/6-311++G** method. Effects of protonation on the bond lengths and angles, and atomic charges, and on their correlations are studied in detail. Results show that the most affected characteristics by protonation are the N–H bond lengths and the charge of the hydrogen atoms. It is found, interestingly, that in the protonation of DAA, electric charges of the unprotonated nitrogen atoms are increased more than that of the protonated nitrogen atoms. Because of very small effects of protonation on the skeletal C–N and N–N bond lengths, it can be said that the aza-adamantane cage volume is not changed significantly upon protonation. The protonation energies approve multivalent nature of these bases with the order of TAA ≈ HAA > DAA. Different isomers for the unprotonated and protonated HAA and DAA are also studied.

Structural and Electronic Properties of Columnar Supramolecular Assemblies Formed from Ionic Metal-Free Phthalocyanine on Au(111)

Highly ordered assemblies prepared from tetra (4-sulfonatophenyl) phthalocyanine (TSPc) by employing very acidic aqueous solutions were deposited onto Au(111) substrates and studied in UHV using X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and orbital mediated tunneling spectroscopy (OMTS). XPS of the TSPc aggregates shows that the ratio of protonated to unprotonated nitrogens does not change with decreasing solution pH. STM images of TSPc deposited from pH <1 solutions reveal ordered branched web-like assemblies hundreds of nanometers in length, generally 2 nm tall and having variable widths. High-resolution UHV-STM images of TSPc aggregates on Au(111) reveal detailed coherent columnar architecture with the phthalocyanine macrocycles orientated parallel to the substrate surface. OMTS was used to identify high-energy occupied orbitals, the LUMO of the TSPc aggregates, and the results are contrasted with the same molecular states in unsubstituted metalated phthalocyanines (M...

Solvation of Nucleobases in 1,3-Dialkylimidazolium Acetate Ionic Liquids: NMR Spectroscopy Insights into the Dissolution Mechanism

NMR studies of uracil, thymine, and adenine dissolved in 1-ethyl-3-methyl-imidazolium acetate ([C(2)mim][CH(3)COO]) and 1-butyl-3-methyl-imidazolium acetate ([C(4)mim][CH(3)COO]) show that hydrogen bonds (HB) dictate the dissolution mechanism and that both cations and anions participate in the solvation process. For that, the 1,3-dialkylimidazolium acetate ionic liquids (ILs) were considered to be bifunctional solvation ionic liquids. In the solvation of uracil and thymine, the [CH(3)COO](-) anion favors the formation of hydrogen bonds with the hydrogen atoms of the N1-H and N3-H groups of the nucleobases, while the aromatic protons in the bulky cations ([C(2)mim](+) and [C(4)mim](+)), especially the most acidic H2, interact with the oxygen atoms of the carbonyl groups. In the adenine solvation, while the [CH(3)COO](-) anion favors the formation of hydrogen bonds with the hydrogen atoms of the amino and N9-H groups of adenine, the aromatic protons in the bulky cations ([C(2)mim](+) and [C(4)mim](+)), especially the most acidic H2, prefer to interact with the unprotonated nitrogen atoms (N1, N3, and N7) of adenine. It is clearly demonstrated that hydrogen bonding is the major driving force in the dissolution of nucleobases in 1,3-dialkylimidazolium acetate ILs. Our results show that the ionic liquid must be a good hydrogen bond acceptor and a moderate hydrogen bond donor to dissolve nucleic acid bases. To strengthen the evidence of the proposed mechanism, NMR studies in the absence of deuterated cosolvents have been used, because the use of deuterated solvents could seriously hinder the dissolving capability of the IL for nucleobases.