Deprotonated Form Research Articles

Comparative equilibrium and structural studies of new pentamethylcyclopentadienyl rhodium complexes bearing (O,N) donor bidentate ligands

Complex formation processes of the (O,N) donor ligands 6-methylpicolinic acid (6-Mepic), quinoline-2-carboxylic acid (2-QA) and 3-isoquinolinecarboxylic acid (3-iQA) with the organometallic moiety (η5-pentamethylcyclopentadienyl)rhodium(III) (RhCp*) were studied in aqueous solution by the combined use of pH-potentiometry, 1H NMR spectroscopy and UV-Vis spectrophotometry. The solid phase structures of the [RhCp*(L)Cl] complexes bearing 6-Mepic and 2-QA were characterized by single-crystal X-ray diffraction analysis. Studies revealed the exclusive formation of mono complexes of the form [RhCp*(L)(H2O)]+ (L = deprotonated form of the ligands) and [RhCp*(L)(OH)]. The positively charged aqua species predominate at physiological pH even in the micromolar concentration range. The H2O/Cl− co-ligand exchange constants showed that all complexes preferably retain the chlorido ligand at the third coordination site at chloride ion concentrations present in the serum. In addition in vitro cytotoxicity of these [RhCp*(L)Cl] complexes was evaluated in three human cancer cell lines (A549, SW480 and CH1/PA-1) where they showed minor cytotoxic potency.

Novel CoIII complexes containing fluorescent coumarin-N-acylhydrazone hybrid ligands: Synthesis, crystal structures, solution studies and DFT calculations

A series of new CoIII complexes of the type [Co(dien)(L1−L3)]ClO4 (1–3), containing fluorescent coumarin-N-acylhydrazonate hybrid ligands, (E)-N′-(1-(7-oxido-2-oxo-2H-chromen-3-yl)ethylidene)-4-R-benzohydrazonate [where R=H (L12−), OCH3 (L22−) or Cl (L32−)], were obtained and isolated in the low spin CoIII configuration. Single-crystal X-ray diffraction showed that the coumarin-N-acylhydrazones act as tridentate ligands in their deprotonated form (L2−). The cation (+1) complexes contain a diethylenetriamine (dien) as auxiliary ligand and their structures were calculated by DFT studies which were also performed for the CoII (S=1/2 and S=3/2) configurations. The LS CoII (S=1/2) concentrated the spin density on the O–Co–O axis while the HS CoII (S=3/2) exhibited a broad spin density distribution around the metallic center. Cyclic voltammetry studies showed that structural modifications made in the L2− ligands caused a slight influence on the electronic density of the metal center, and the E1/2 values for the CoIII/CoII redox couple increased following the electronic effect of the R-substituent, in the order: 2 (R=OCH3)<1 (R=H)<3 (R=Cl). The theoretical redox potentials (E°) of the process CoIII→CoII were calculated for both CoII spin states (S=1/2 and S=3/2) and a better correlation was found for CoIII→CoII (S=1/2), compared with experimental values vs SHE (E°calc=−0.37, −0.36 and −0.32V vs E°exp.=−0.371, −0.406 and −0.358V, for 1–3 respectively). Complexes 1–3 exhibited a very intense absorption band around 470nm, assigned by DFT calculations as π-π* transitions from the delocalized coumarin-N-acylhydrazone system. 1–3 were very stable in MeOH for several days. Likewise, 1–3 were stable in phosphate buffer containing sodium ascorbate after 15h, which was attributed to the high chelate effect and σ-donor ability of the L2− and dien ligands.

Canonical, Deprotonated, or Zwitterionic? A Computational Study on Amino Acid Interaction with the TiO2 (101) Anatase Surface

The interaction of 11 amino acids with the TiO2 (101) anatase surface was investigated by means of PBE-D2* periodic simulations, both from a static and dynamic points of view. Several adsorption states, with the amino acid in its canonical, zwitterionic, or deprotonated forms, were considered. The strongest interactions correspond to dative interactions between the electron pairs of N or O atoms of the amino acids and the Ti atoms of the surface. For glycine, the most stable configuration corresponds to the deprotonated (N,O) binding mode, at variance to that observed for the adsorption of glycine on rutile (110) surface, for which the dissociative (O,O) binding mode was determined to be the preferred one. For the remaining amino acids, the following general trend was identified: those amino acids with acidic or a basic lateral chain groups, except Arg, exhibit a deprotonated (N,O) binding mode as glycine, because the additional dative interactions with the side chain overcome the destabilizing effect ind...

Roles of the Active Site Zn(II) and Residues in Substrate Discrimination by Threonyl-tRNA Synthetase: An MD and QM/MM Investigation.

Threonyl-tRNA synthetase (ThrRS) is a Zn(II) containing enzyme that catalyzes the activation of threonine and its subsequent transfer to the cognate tRNA. This process is accomplished with remarkable fidelity, with ThrRS being able to discriminate its cognate substrate from similar analogues such as serine and valine. Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) methods have been used to elucidate the role of Zn(II) in the aminoacylation mechanism of ThrRS. More specifically, the role of Zn(II) and active site residues in ThrRS's ability to discriminate between its cognate substrate l-threonine and the noncognate l-serine, l-valine, and d-threonine has been examined. The present results suggest that a role of the Zn(II) ion, with its Lewis acidity, is to facilitate deprotonation of the side chain hydroxyl groups of the aminoacyl moieties of cognate Thr-AMP and noncognate Ser-AMP substrates. In their deprotonated forms, these substrates are able to adopt a conformation preferable for aminoacyl transfer from aa-AMP onto the Ado-3'OH of the tRNAThr cosubstrate. Relative to the neutral substrates, when the substrates are first deprotonated with the assistance of the Zn(II) ion, the barrier for the rate-limiting step is decreased significantly by 42.0 and 39.2 kJ mol-1 for l-Thr-AMP and l-Ser-AMP, respectively. An active site arginyl also plays a key role in stabilizing the buildup of negative charge on the substrate's bridging phosphate oxygen during the mechanism. For the enantiomeric substrate analogue d-Thr-AMP, product formation is highly disfavored, and as a result, the reverse reaction has a very low barrier of 16.0 kJ mol-1.

Synthesis, crystal structures, and catalytic properties of two oxidovanadium(V) complexes with tridentate Schiff bases

Two new oxidovanadium(V) complexes, [VO2L1] (I) and [VO2L2] (II), where L1 and L2 are the deprotonated forms of 4-methyl-2-[(2-morpholin-4-ylethylimino)methyl]phenol (HL1) and 2-[(2-isopropylaminoethylimino) methyl]-4-trifluoromethoxyphenol (HL2), respectively, have been prepared and characterized by physico chemical methods and single crystal X-ray diffraction (CIF files CCDC nos. 1443671 (I), 1443672 (II)). The V atom in each complex is coordinated by the phenolate oxygen, imino nitrogen and amino nitrogen of the Schiff base ligand, and two oxo groups, forming trigonal-bipyramidal geometry. The oxidation of olefins with the complexes as catalyst was evaluated, which indicated that both complexes showed effective catalytic efficiency in oxidation of several aliphatic and aromatic substrates by using tert-butyl hydrogen peroxide as oxidant.

N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase.

The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H]+ and [pCyd+H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over the IR fingerprint and hydrogen-stretching regions complemented by electronic structure calculations. The low-energy conformations of [pdCyd+H]+ and [pCyd+H]+ and their relative stabilities are computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers allow the conformers present in the experiments to be determined. Similar to that found in previous IRMPD action spectroscopy studies of the protonated forms of the cytosine nucleosides, [dCyd+H]+ and [Cyd+H]+, both N3 and O2 protonated cytosine mononucleotides exhibiting an anti orientation of cytosine are found to coexist in the experimental population. The 2'-hydroxyl substituent does not significantly influence the most stable conformations of [pCyd+H]+ versus those of [pdCyd+H]+, as the IRMPD spectral profiles of [pdCyd+H]+ and [pCyd+H]+ are similar. However, the presence of the 2'-hydroxyl substituent does influence the relative intensities of the measured IRMPD bands. Comparisons to IRMPD spectroscopy studies of the deprotonated forms of the cytosine mononucleotides, [pdCyd-H]- and [pCyd-H]-, provide insight into the effects of protonation versus deprotonation on the conformational features of the nucleobase and sugar moieties. Likewise, comparisons to results of IRMPD spectroscopy studies of the protonated cytosine nucleosides provide insight into the influence of the phosphate moiety on structure. Comparison with previous ion mobility results shows the superiority of IRMPD spectroscopy for distinguishing various protonation sites. Graphical Abstract ᅟ.

Evidence from FTIR Difference Spectroscopy That a Substrate H2O Molecule for O2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn4CaO5 Cluster.

The O2-producing Mn4CaO5 catalyst in photosystem II oxidizes two water molecules (substrate) to produce one O2 molecule. Considerable evidence supports the identification of one of the two substrate waters as the Mn4CaO5 cluster's oxo bridge known as O5. The identity of the second substrate water molecule is less clear. In one set of models, the second substrate is the Mn-bound water molecule known as W2. In another set of models, the second substrate is the Ca2+-bound water molecule known as W3. In all of these models, a deprotonated form of the second substrate moves to a position next to O5 during the catalytic step immediately prior to O-O bond formation. In this study, FTIR difference spectroscopy was employed to identify the vibrational modes of hydrogen-bonded water molecules that are altered by the substitution of Sr2+ for Ca2+. Our data show that the substitution substantially altered the vibrational modes of only a single water molecule: the water molecule whose D-O-D bending mode is eliminated during the catalytic step immediately prior to O-O bond formation. These data are most consistent with the identification of the Ca2+-bound W3 as the second substrate involved in O-O bond formation.

Steric Enforcement about One Thiolate Donor Leads to New Oxidation Chemistry in a NiSOD Model Complex

Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to the presence of oxygen-sensitive Ni-SCys bonds at its active site. Reported in this account is the synthesis and properties of the NiII complex of the N3S2 ligand [N3S2Me2]3- ([N3S2Me2]3- = deprotonated form of 2-((2-mercapto-2-methylpropyl)(pyridin-2-ylmethyl)amino)-N-(2-mercaptoethyl)acetamide), namely Na[Ni(N3S2Me2)] (2), as a NiSOD model that features sterically robust gem-(CH3)2 groups on the thiolate α-C positioned trans to the carboxamide. The crystal structure of 2, coupled with spectroscopic measurements from 1H NMR, X-ray absorption, IR, UV-vis, and mass spectrometry (MS), reveal a planar NiII (S = 0) ion coordinated by only the N2S2 basal donors of the N3S2 ligand. While the structure and spectroscopic properties of 2 resemble those of NiSODred and other models, the asymmetric S ligands open up new reaction paths upon chemical oxidation. One unusual oxidation product is the planar NiII-N3S complex [Ni(Lox)] (5; Lox = 2-(5,5-dimethyl-2-(pyridin-2-yl)thiazolidin-3-yl)-N-(2-mercaptoethyl)acetamide), where two-electron oxidation takes place at the substituted thiolate and py-CH2 carbon to generate a thiazolidine heterocycle. Electrochemical measurements of 2 reveal irreversible events wholly consistent with thiolate redox, which were identified by comparison to the ZnII complex Na[Zn(N3S2Me2)] (3). Although no reaction is observed between 2 and azide, reaction of 2 with superoxide produces multiple products on the basis of UV-vis and MS data, one of which is 5. Density functional theory (DFT) computations suggest that the HOMO in 2 is π* with primary contributions from Ni-dπ/S-pπ orbitals. These contributions can be modulated and biased toward Ni when electron-withdrawing groups are placed on the thiolate α-C. Analysis of the oxidized five-coordinate species 2ox* by DFT reveal a singly occupied spin-up (α) MO that is largely thiolate based, which supports the proposed NiIII-thiolate/NiII-thiyl radical intermediates that ultimately yield 5 and other products.

3-D Topo Surface Visualization of Acid–Base Species Distributions: Corner Buttes, Corner Pits, Curving Ridge Crests, and Dilution Plains

Species TOPOS is a free software package for generating three-dimensional (3-D) topographic surfaces (“topos”) for acid–base equilibrium studies. This upgrade adds 3-D species distribution topos to earlier surfaces that showed pH and buffer capacity behavior during titration and dilution procedures. It constructs topos by plotting computed α values above a composition grid with volume of NaOH added as the x axis and overall system dilution as the y axis. The systematic shift from protonated to deprotonated forms is clearly visualized on a linear z axis. Because pH and buffer capacity surfaces accompany the species topos, it is easy to see their interrelationships. On the basis of their graphical appearance, features on species topos have been named corner buttes, corner pits, curving ridge crests, and dilution plains. Ramps connecting surface features are linear when tied to additions of NaOH and logarithmic when associated with the logarithmic dilution axis. The amphiprotic behavior of water is demonstra...

Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis.

In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimental information, these molecules were created by altering protonation states (singly protonated, doubly protonated, or doubly deprotonated) and number of their ligands. The energetics of the I'N2O4, and I'NO2 and their analogues predicted that both stepwise and concerted mechanisms occurred either with similar barriers, or the latter was more favorable than the former. They also showed that the doubly deprotonated form hydrolyzed the peptide bond with substantially lower barriers than the barriers for other protonation states. For NO2 core possessing complexes, Zr-(NO2)(OHH)(H2O/OH)n for n = 1-3, the hydroxyl group containing molecules were found to be more reactive than their water ligand possessing counterparts. The barriers for these complexes reduced with an increase in the coordination number (6-8) of the Zr(IV) ion. Among all 11 molecules, the NO2 core possessing and two hydroxyl group containing I'DNO2-2H complex was found to be the most reactive complex with a barrier of 28.9 kcal/mol. Furthermore, barriers of 27.5, 28.9, and 32.0 kcal/mol for hydrolysis of Gly-Glu (negative), Gly-Gly (neutral), and Gly-Lys (positive) substrates, respectively, by this complex were in agreement with experiments. The activities of these complexes were explained in terms of basicity of their ligand environment and nucleophilicity of the Zr(IV) center using metal-ligand distances, charge on the metal ion, and the metal-nucleophile distance as parameters. These results provide a deeper understanding of the functioning of these complexes and will help design Zr(IV)-based synthetic metallopeptidases.

Cyclometalated Platinum(II) Complexes Comprising 2‐(Diphenylphosphino)pyridine and Various Thiolate Ligands: Synthesis, Spectroscopic Characterization, and Biological Activity

The known cyclometalated platinum(II) complex [Pt(ppy)(DMSO)(Cl)] (A) in which ppy = 2‐phenylpyridinate, was treated with 2‐(diphenylphosphino)pyridine (PPh2py, PN) (1 equiv.) and readily afforded complex [Pt(ppy)(PPh2py‐κ1P)(Cl)] (1). The transphobia effect (T) and single‐crystal X‐ray diffraction crystallography confirmed that the phosphine ligand in 1 is located trans to the nitrogen atom of the cyclometalating fragment (ppy). Compound 1 was treated with various thiolate reagents (1 equiv.) at room temperature, leading to the displacement of the chloride ligand in 1 by thiolate ligands through a salt metathesis reaction. The reaction led to the formation of a series of monomeric complexes with the general formula [Pt(ppy)(PPh2py‐κ1P)(SR)] (2a–2d), where SR = deprotonated form of pyridine‐2‐thiol (HSpy, 2a), pyrimidine‐2‐thiol (HSpyN, 2b), thiophenol (HSPh, 2c), and 2‐thiazoline‐2‐thiol (HSt, 2d). All complexes have been characterized by NMR spectroscopy. The biological activities of the complexes were evaluated against three human cancer cell lines, including A549 (human lung cancer), SKOV3 (human ovarian cancer), and MCF7 (human breast cancer), by means of the MTT assay [MTT = 3‐(4,5‐dimethylthiazol‐yl)‐2,5‐diphenyltetrazolium bromide]. Compounds 2a and 2b presented effective, potent cytotoxic activity regarding the cell lines. Electrophoretic mobility shift assays on plasmid DNA and molecular modeling investigations were also performed to determine the specific binding mode or the binding orientation of the complexes to DNA.

Open-chain hemiketal is stabilized by coordination to a copper (II)

The hemiketal complex [Cu{NH2C(Me)2C(Ph)(OMe)O}2] (1) was generated by the reaction of [Cu(NCMe)4](BF4) and 4 equivs of 2,2-dimethyl-3-phenyl-2H-azirine in the presence of NCNMe2 in wet MeOH and isolated in 92% yield. In 1, the in situ formed hemiketal NH2C(Me)2C(Ph)(OMe)OH in its deprotonated form is stabilized due to chelation to copper(II). In the X-ray structure of 14MeOH, the intermolecular hydrogen bonding was detected between O and N atoms of the organic ligand and the HO group of solvated MeOH as well as between two molecules of the solvated MeOH. Three types of hydrogen bonds in the obtained structure were studied by the DFT calculations (M06/6-31++G** level of theory, MDF10 pseudopotentials on the Cu atoms) and topological analysis of the electron density distribution within the formalism of Bader's theory (QTAIM method). Estimated strength of these non-covalent interactions is 3–9kcal/mol.

Synthesis, characterization, and crystal structures of mononuclear and dinuclear copper(II) complexes derived from similar tridentate Schiff bases

ABSTRACTA mononuclear copper(II) complex, [CuL1N3] (1), and a dinuclear copper(II) complex, [Cu2(L2)2(μ1,1-N3)2] (2), where L1 and L2 are the deprotonated forms of 2-[(2-diethylaminoethylimino)methyl]-4,6-difluorophenol (HL1) and 2,4-difluoro-6-[(2-isopropylaminoethylimino)methyl]phenol (HL2), respectively, were prepared. The complexes were characterized by elemental analysis, infrared (IR) and UV–Vis spectra, and single crystal X-ray determination. The crystal of complex 1 crystalizes in the orthorhombic space group Pbca, with unit cell a = 6.9327(7), b = 13.8926(13), c = 31.243(2) Å, V = 3009.1(5) Å3, Z = 8. The crystal of complex 2 crystalizes in the monoclinic space group P21/n, with unit cell a = 20.8686(16), b = 9.4893(16), c = 7.2440(12) Å, β = 94.020(2)°, V = 1431.0(4) Å3, Z = 4. The Cu atom in complex 1 is in square planar geometry, and that in complex 2 is in square pyramidal geometry.

Simulation of the UV/Visible Absorption Spectra of Fluorescent Protein Chromophore Models

AbstractTime‐dependent density functional theory has been used to simulate the UV/Vis absorption spectra of fluorescent protein model chromophores with particular focus on the vibronic structure of the lowest‐energy absorption band as a structural fingerprint. Combining the B3LYP‐35 XC functional with non‐equilibrium solvation and the gradient approach provides a vibronic structure close to that recorded experimentally (when comparisons with experiment are possible). This study focuses on the chromophore present in green fluorescent proteins (FP1), in its neutral and deprotonated forms as well as for both cis (Z) and trans (E) conformations. The method was then employed to simulate the spectra of structures for which experimental spectra are not available or not well resolved. The effect of extending the conjugation of the chromophore, by adding unsaturated moieties such as in the chromophore of DsRed (FP2), was considered. Overall, among these three investigated structural modifications (neutral versus anionic, smaller versus larger chromophore, and cis versus trans conformations), absorption spectra can only distinguish unambiguously between the neutral and anionic forms. An extension of the π‐conjugation length of the chromophore is, as would be expected, reflected in a bathochromic shift of the absorption band maximum, but modifications of the chromophore environment in proteins can also induce shifts of the absorption maximum, and they are difficult to distinguish from each other.

Synthesis and Speciation-Dependent Properties of a Multimetallic Model Complex of NiSOD That Exhibits Unique Hydrogen-Bonding

The complex Na3[{NiII(nmp)}3S3BTAalk)] (1) (nmp2- = deprotonated form of N-(2-mercaptoethyl)picolinamide; H3S3BTAalk = N1,N3,N5-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S3BTAalk), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and 1H NMR measurements on 1 indicate that the NiII centers are square-planar with N2S2 coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm-1 shift in νNH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1A; λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. Dissolution of 1 in pH 7.4 buffer or in unbuffered water at temperatures above 50 °C results in monomeric complex (1M; λ = 367 nm) linked through intramolecular NH···S bonds. DFT computations indicate a low energy barrier between 1A and 1M with nearly identical frontier MOs and Ni-ligand metrics. Notably, 1A and 1M exhibit remarkable stability in protic solvents such as MeOH and H2O, in stark contrast to monometallic [NiII(nmp)(SR)]- complexes. The reactivity of 1 with excess O2, H2O2, and O2•- is species-dependent. IR and UV-vis reveal that 1A in MeOH reacts with excess O2 to yield an S-bound sulfinate, but does not react with O2•-. In contrast, 1M is stable to O2 in pH 7.4 buffer, but reacts with O2•- to yield a putative [NiII(nmp)(O2)]- complex from release of the BTA-thiolate based on EPR.

Investigating the pH Dependence of Ultraviolet Radiation Induced Synthesis of TiO&lt;sub&gt;2&lt;/sub&gt;/Poly(Acrylic Acid) Nanocomposites

In this work, Poly(Acrylic Acid) (PAA) was employed as nanoparticle stabilizer for TiO2. Adsorption and encapsulation of nanoparticles in polyelectrolytes impart stability due to stearic and electrostatic effects. Crosslinking of the polymer through UV-Irradiation permanently encapsulates the metal as well as reinforces the polymer cage. The efficient pH and ratio of reactants were optimized then assessed through Dynamic Light Scattering (DLS) for particle size and Zeta Potential Measurements for stability in aqueous solutions. Results showed that among the various TiO2/PAA ratios, the 1:3 ratio showed minimal changes on the size and Zeta Potential values even when exposed to various pH conditions. Meanwhile at pH 5, TiO2 attained a positive surface charge, while PAA exists in its deprotonated form, thus maximizing the electrostatic interaction between the two materials. Analysis revealed that in that particular ratio and pH range, particles size and zeta-potential value of 61.79 nm and -36 mV were obtained respectively. Physical morphology of the nanocomposites was characterized through Scanning Electron Microscopy, showing agglomerates of small particles, resulting to larger particles. Further studies shall be done to utilize the potential of the polymer-coated nanoparticles in dry form.

Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance.

Pinonic acid, a C10-monocarboxylic acid with a hydrophilic -CO2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene - an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of the cis-pinonate anion (cPA-), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA- can adopt two different structural configurations - open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The added waters, which mainly interact with the negatively charged -CO2- group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analyses suggest that the mono- and di-hydrates are likely to exist in humid atmospheric environments with high populations. The detailed molecular description of cPA- hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.

Low-spin [MII(L)2] and [MIII(L)2]+ (M = Fe and Co) complexes of tridentate azo-containing pyridine/pyrazine amide ligands: structures, properties and redox potential correlations.

Using deprotonated forms of tridentate azo-containing pyridine-2-/pyrazine-2-carboxamide 2-[N-(2-phenylazo)carbamoyl]-pyridine/pyrazine, seven bis-ligand complexes of FeII/CoII and FeIII/CoIII have been synthesized. Molecular structures of six of them reveal that these six-coordinate complexes utilize all available donor sites of the ligands and assume MII/IIIN2(pyridine/pyrazine)N'2(amide)N''2(azo) coordination. Complexes of FeII and CoIII are diamagnetic and those of FeIII and CoII are paramagnetic (S = 1/2; room-temperature magnetic data and EPR spectra). Cyclic voltammetry experiments in CH2Cl2 reveal facile metal-centred FeIII/FeII and CoIII/CoII redox responses, and all complexes display quasireversible-to-irreversible ligand(azo)-centred redox processes. The E1/2 values of MIII/MII redox processes for Fe, Co and Ni (reported earlier) complexes of the pyridine amide ligand linearly correlate with those for six-coordinate [MIII(bpy)3]3+/[MII(bpy)3]2+, [MIII(terpy)2]3+/[MII(terpy)2]2+, [MIII(L)]+/[MII(L)]0 or [MIII(L')2]+/[MII(L')2]0 (bpy = 2,2'-bipyridine, terpy = 2,2':6',2''-terpyridine, hexadentate L(2-) = 1,4-bis[o-(pyridine-2-carboxamidophenyl)]-1,4-dithiobutane and tridentate L'(-) = {2-[2-(arylimino)phenylazo]-pyridine}) couples. Density functional theory (DFT) at the B3LYP level and time-dependent (TD)-DFT calculations rationalize the electronic structure of the present complexes and throw light on the origin of observed electronic transitions.

Coordination properties of molecular and anionic forms of 5,10,15,20,21-pentaphenyl-2,3,7,8,12,13,17,18-octaethylporphyrin in acetonitrile

Acid and coordination properties of 5,10,15,20,21-pentaphenyl-2,3,7,8,12,13,17,18-octaethylporphine in 1,8-diazabicyclo[5.4.0]undec-7-ene–acetonitrile system at 298 K have been studied by spectrophotometric titration. It has been found that titration causes deprotonation of nitrogen atom of the pyrrole ring to produce monodeprotonated form. Acid dissociation constant of the compound in 1,8-diazabicyclo[5.4.0]undec-7-ene–acetonitrile system at 298 K has been determined. Complexation of molecular and deprotonated forms of the ligand with silver nitrate has been studied, kinetic parameters of the corresponding reactions have been obtained. Kinetics of silver complexation with the studied ligand by ionic and molecular mechanism has been analyzed.

The intrinsic basicity of the phosphate backbone exceeds that of uracil and thymine residues: protonation of the phosphate moiety is preferred over the nucleobase for pdThd and pUrd.

The gas-phase conformations of the protonated forms of thymidine-5'-monophosphate and uridine-5'-monophosphate, [pdThd+H]+ and [pUrd+H]+, are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure calculations. The IRMPD action spectra of [pdThd+H]+ and [pUrd+H]+ are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Low-energy conformations of [pdThd+H]+ and [pUrd+H]+ and their relative stabilities are computed at the MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers indicate that the dominant conformers of [pdThd+H]+ and [pUrd+H]+ populated in the experiments are protonated at the phosphate oxo oxygen atom, with a syn nucleobase orientation that is stabilized by strong P[double bond, length as m-dash]OH+O2 and P-OHO4' hydrogen-bonding interactions, and C2'-endo sugar puckering. Minor abundance of conformers protonated at the O2 carbonyl of the nucleobase residue may also contribute for [pdThd+H]+, but do not appear to be important for [pUrd+H]+. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of thymidine and uridine, [dThd+H]+ and [Urd+H]+, and the deprotonated forms of pdThd and pUrd, [pdThd-H]- and [pUrd-H]-, provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Most interestingly, the thymine and uracil nucleobases remain in their canonical forms for [pdThd+H]+ and [pUrd+H]+, unlike [dThd+H]+ and [Urd+H]+, where protonation occurs on the nucleobases and induces tautomerization of the thymine and uracil residues.