Thermodynamic cycle for the calculation of ab initio pKa values for hydroxamic acids

A thermodynamic cycle to calculate pK_a values (Minus log of acid dissociation constants) of hydroxamic acids is presented. Hydroxamic acids exist mainly as amide isomers in the aqueous medium. The amide form of hydroxamic acids has two deprotonation sites and may yield either an N-ion or an O-ion upon deprotonation. The thermodynamic cycle proposed includes the gas-phase N–H deprotonation of the hydroxamic acid, the solvent phase transformation of the N-ion to the O-ion and the solvation of the hydroxamic acid molecule and the O-ion in water. The CBS-QB3 method was employed to obtain gas-phase free energy differences between 12 hydroxamic acids and their respective anions. The aqueous solvation Gibbs free energy changes were calculated at the HF/6-31G(d)/CPCM and HF/6-31+G(d)/CPCM levels of theory using HF/6-31+G(d)/CPCM geometries. For the proton, literature values of the gas-phase free energy of formation and the solvation free energy change were used. The free energy change for the transformation of the N-ion to O-ion in the aqueous medium was calculated by employing CBS-QB3/CPCM in the aqueous medium. For this, the hydroxamic acids were divided in two classes according to the substituent at the carbonyl carbon. A common transformation free energy difference for aliphatic substituted hydroxamic acids and a separate common transformation free energy difference for aromatic substituted hydroxamic acids were obtained. The pK_a calculation yielded a root mean square error of 0.32 pK_a units.     

Quantum-chemical calculations of the methylation of hydroxamic and thiohydroxamic acids with diazomethane

We made calculations about the methylation of both hydroxamic and thiohydroxamic acids with CH₂N₂. The potential-energy surfaces of several proposed pathways leading to possible site-selective products (N-methylated and O-methylated hydroximates) are presented. Our results agree satisfactorily with an experimental observation by Liguori et al. who found site selectivity in the formation of dimethylated products. Simultaneous deprotonation and methylation occurs in both forms (E and Z) of hydroxamic acid and thiohydroxamic acid, and the net energy barrier via this pathway is the smallest. In most corresponding processes the energy barriers are smaller for thiohydroxamic acid, and the Z-form has an energy barrier smaller than that of the E-form in both hydroxamic and thiohydroxamic acids.     

Vibrational spectra and density functional study of propylgermane

Raman and infrared spectra of propylgermane, CH₃CH₂CH₂GeH₃, and its Ge-deuterated analog, CH₃CH₂CH₂GeD₃, were investigated in their gaseous, liquid and solid states. The normal coordinate treatment was carried out by density functional theory (DFT) calculation, using B3LYP/6-31G^* and 6-311++G^** basis sets, and the corresponding fundamental vibrations were assigned. The trans (T) and gauche (G) forms around the central C–C bond coexisted in the gaseous and liquid states and only the T form existed in the solid state. From the temperature dependent measurements of the Raman spectra in the liquid state, the enthalpy difference was found to be ΔH(T−G)=−0.36±0.02 kcalmol⁻¹ with the T form being more stable. The energy differences between the isomers obtained by DFT calculations were ΔE(T−G)=−0.46 kcalmol⁻¹ and ΔE(T−G)=−0.87 kcalmol⁻¹ by the 6-31G^* basis set and 6-311++G^** basis set, respectively.     

Comprehensive density functional theory study on serine and related ions in gas phase: conformations, gas phase basicities, and acidities

Density functional theory (DFT) calculations have been performed to investigate the gas-phase conformations of serine and its three related ions (serineH(+), serine(-), and serine(2-)). The full ensemble of possible conformations, 324 conformations for serine, 108 for serineH(+), 162 for serine(-) and 54 for serine(2-), were first surveyed at B3LYP/6-31G level, and then the obtained unique conformations were further refined at B3LYP/6-311+G level. From full optimizations, 74 unique conformations for seine, 14 for serineH(+), 11 for serine(-), and 4 for serine(2-) were located, and their relative energies were also determined at B3LYP/6-311+G level. Atoms in molecules (AIM) analysis was carried out to establish rigorous definition of hydrogen bonds. Six types of intramolecular H-bonds in conformers of serine, six types in serineH(+), three types in serine(-), and two types in serine(2-) were identified within the framework of AIM theory and their relative strengths were determined based on topological properties at bond critical points (BCPs) of H-bonds. The intramolecular H-bonds were demonstrated to play an important role in deciding the relative stability of conformations of amino acids and the related ions. The enthalpies and Gibbs free energies of protonation and deprotonation reactions of serine and its related ions were calculated at B3LYP/6-311+G//B3LYP/6-31G, and B3LYP/6-311+G//B3LYP/6-311+G level. The calculated results are both in excellent agreement with the experimental data. We demonstrate in this study that B3LYP is an efficient and accurate method to predict the thermochemical and structural parameters of amino acids and the related ions.     

Proton-bound homodimers: how are the binding energies related to proton affinities?

High-level quantum chemical calculations [G3(MP2)-RAD//MP2/6-31+G(d,p)] have been employed to investigate the relationship between the binding energy (BE) of a substrate (X) and its protonated form [H-X]+ with the proton affinity (PA) of the substrate (X) in several series of protonated homodimers ([X...H-X]+). We find that for each series of closely related substrates, the binding energy (BE) is correlated with the proton affinity (PA) in an approximately quadratic manner. Thus, for a given series, the BE initially increases in magnitude with increasing PA, reaches a point of maximum binding, and then becomes smaller as the PA increases further. This behavior can be attributed to the competing effects of the exothermic partial protonation of the substrate and the endothermic partial deprotonation of the protonated substrate. As the PA increases, protonation of X contributes to increased binding but the penalty for partial deprotonation of [H-X]+ also increases. Once the PA becomes sufficiently high, the penalty for the partial deprotonation of [H-X]+ dominates, leading to maximum binding occurring at intermediate PA.     

N‐[(Diphenoxyphosphoryl)oxy]‐2‐phenyl‐1H‐benzimidazole as a versatile reagent for synthesis O‐alkylhydroxamic acids

Highly efficient reagent, N‐[(diphenoxyphosphoryl)oxy]‐2‐phenyl‐1H‐benzimidazole was synthesized and its applicability was demonstrated for the synthesis of O‐alkyl hydroxamic acids. The efficiency of the reagent was evaluated through the synthesis of range of O‐alkyl hydroxamic acids from aromatic carboxylic acids as well as N‐protected amino acids. The enatiomeric purity of synthesized compounds was measured using chiral HPLC and the degree of racemization that occurred was found to be negligible.     

Kinetic study of proton-transfer reactions of phenylnitromethanes. Implication for the origin of nitroalkane anomaly

Measurements of rate constants and substituent effects for three important elementary steps of proton-transfer reactions of phenylnitromethane were reported. The Hammett ρ values for the deprotonation of ArCH(2)NO(2) with OH(-), protonation of ArCH═NO(2)(-) with H(2)O, and protonation of ArCH═NO(2)(-) with HCl were determined in aqueous MeOH at 25 °C. Comparison of these experimentally observed ρ values with those calculated at B3LYP/6-31G* revealed that aci-nitro species (ArCH═NO(2)H), which is formed on the O-protonation of ArCH═NO(2)(-), does not lie on the main route of the proton-transfer reaction. Analysis of the Br?nsted plot implies that the proton-transfer reaction of most XC(6)H(4)CH(2)NO(2) exhibits nitroalkane anomaly, but not for p-NO(2)C(6)H(4)CH(2)NO(2), and that the transition state charge imbalance is an origin of anomaly.     

Acidity of hydroxamic acids and amides

The relatively strong acidity of hydroxamic acids was analyzed by means of isodesmic reactions in which this acid or its anion is formed from simpler precursors. Acidity of amides was analyzed in the same way. Energies of all compounds involved in the reactions were calculated at the B3LYP/AUG-cc-pVTZ//B3LYP/6-311 + G(d,p) level; at this level a good agreement was reached with the sparse experimental data. Interpretation of the results was the same as in the recent discussion of the acidity of carboxylic acids, and the conclusions were similar: both amides and hydroxamic acids are stabilized with respect to simpler reference molecules of amines or N-alkylhydroxylamines, respectively. However, their anions are stabilized still more and are responsible for the acidity. This effect is stronger in hydroxamic acids or amides than in carboxylic acids. The problem of whether it is due to resonance depends on the definition of this term. Semiquantitative comparison suggests that resonance in hydroxamic acids is more important than in amides and still more than in carboxylic acids. The stronger acidity of hydroxamic acids compared to amides is due to the destabilizing inductive effect of the hydroxyl group in the acid molecule, not to any effect in the anion.     

A thermochemical investigation of guest-host interactions in labile Werner clathrates of the [Ni(4-EtPy)4(NCS)2]·G type (G = Methyl derivatives of benzene)

The stoichiometry of thermal decomposition has been studied for (I): [Ni(4-EtPy)₄(NCS)₂] as a host complex as well as for its clathrates [Ni(4-EtPy)₄(NCS)₂]·G where guest molecule G - toluene, (II): T, (III): o-xylene (o-X) and (IV): p-xylene (p-X). The loss of volatile components proceeds in three steps (−2L, −1L, −1L) for I and in four steps (−G, −2L, −1L, −1L) for II, III and IV. DSC and X-ray powder measurements indicated a phase transition in all compounds under study. However, this process is overlapped by the escape of G in II and III. The differences in enthalpy changes are associated with different guest-host interactions in the particular clathrates.     

A theoretical study on NH bond dissociation enthalpies of oxo, thio and seleno carbamates and their N-protonated and N-deprotonated species

The effect of N-protonation and N-deprotonation on structure, NH bond dissociation enthalpies (BDEs) and stabilities of radicals formed on H-abstraction from nitrogen atom of carbamates and their thio- and seleno-analogs have been investigated. For those molecules where experimental results are available for comparison, the ROB3LYP/6-311++G(d,p)//B3LYP/6-31+G* theoretical level is in agreement within the estimated experimental uncertainty. The NH BDE of carbamates H₂NC(=X)YCH₃ [X = O; Y = O, S, Se] are higher but lower when X = S, Se and Y = O, S, Se in comparison to NH BDE of NH₃. DFT calculations indicate that the NH bond dissociation enthalpies are decreased by protonation and deprotonation at nitrogen atom; but the effect of deprotonation is rather smaller than the protonation. The variations are analyzed in terms of stabilities of molecules, their protonated and deprotonated species along with their respective radicals. The electron delocalization from nitrogen, X and Y atoms, electrostatic interactions, conjugative interactions and spin delocalization are the important factors affecting the stability. The spin delocalization and shift of radical center to chalcogen X (X = S, Se) are the main determinants for radical stability.     

Copper(II) 12-metallacrown-4 complexes of alpha-, beta- and gamma-aminohydroxamic acids: a comparative thermodynamic study in aqueous solution

A complete thermodynamic study of the protonation and Cu(II) complex formation equilibria of a series of alpha- and beta-aminohydroxamic acids in aqueous solution was performed. The thermodynamic parameters obtained for the protonation of glycine-, (S)-alpha-alanine-, (R,S)-valine-, (S)-leucine-, beta-alanine- and (R)-aspartic-beta-hydroxamic acids were compared with those previously reported for gamma-amino- and (S)-glutamic-gamma-hydroxamic acids. The enthalpy/entropy parameters calculated for the protonation microequilibria of these three types of ligands are in very good agreement with the literature values for simple amines and hydroxamic acids. The pentanuclear complexes [Cu5L4H(-4)]2+ contain the ligands acting as (NH2,N-)-(O,O-) bridging bis-chelating and correspond to 12-metallacrown-4 (12-MC-4) which are formed by self-assembly between pH 4 and 6 with alpha-aminohydroxamates (HL), while those with beta- and gamma-derivatives exist in a wider pH range (4-11). The stability order of these metallomacrocycles is beta- > alpha- > gamma-aminohydroxamates. The formation of 12-MC-4 with alpha-aminohydroxamates is entropy-driven, and that with beta-derivatives is enthalpy-driven, while with gamma-GABAhydroxamate both effects occur. These results are interpreted on the basis of specific enthalpies or entropy contributions related to chelate ring dimensions, charge neutralization and solvation-desolvation effects. The enthalpy/entropy parameters of 12-MC-4 with alpha-aminohydroxamic acids considered are also dependent on the optical purity of the ligands. Actually, that with (R,S)-valinehydroxamic acid presents an higher entropy and a lower enthalpy value than those of enantiopure ligands, although the corresponding stabilities are almost equivalent. Moreover, DFT calculations are in agreement with a more exothermic enthalpy found for metallacrowns with enantiomerically pure ligands.     

Site selectivity in the synthesis of O-methylated hydroxamic acids with diazomethane

In this paper we report the results obtained by treating some selected hydroxamic acids with diazomethane in ethereal media. The multitask reagent diazomethane was used either as a base to induce deprotonation of the chosen hydroxamic acids or as conjugated acid which undergoes one-pot methylation processes of the generated anions. Product distributions clearly showed that a high site selectivity is expressed by the different deprotonated species in the alkylation processes. Under the adopted conditions, the prevalent site of methylation is in all the cases the oxygen of the hydroxamic acid. While in aliphatic hydroxamic acids only O-alkylation is observed, in the aromatic substrates, the NH group competes with the OH function as the nucleophilic site, although the OH reactivity still dominates.     

Proton affinity of uracil. A computational study of protonation sites

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied computationally with the B3LYP, MP2, QCISD, and QCISD(T) methods and with basis sets expanding from 6-31G(d,p) to 6-311+G(3df,2p). In accordance with a previous density functional theory study, the dioxo tautomer 1a was the most stable uracil isomer in the gas phase. Gibbs free energy calculations using effective QCISD(T)/6-311+G(3df,2p) energies suggested >99.9% of 1a at equilibrium at 523 K. The most stable ion isomer corresponded to N-1 protonated 2,4-dihydroxypyrimidine, which however is not formed by direct protonation of 1a. The topical proton affinities in 1a followed the order O-8 > O-7 > C-5 > N-3 > N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol⁻¹ at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.     

Density functional study of the conformations and intramolecular proton transfer in thiohydroxamic acids

The conformational preferences of thiohydroxamic acids (N-hydroxythioamides) are investigated by the density functional B3LYP/6-311++G(3df,3pd)//B3LYP/6-31G(d) method in this work. Unlike hydroxamic acids, the thione and thiol forms are found to be equally stable in the gas phase, and the reaction pathways for the interconversion between the thione and thiol forms have been deduced to involve rotation about the C[double bond, length as m-dash]N bond of the thiol tautomer in the rate-determining step. The effect of aqueous solvation on the reactions has also been investigated. It is found that inclusion of a few explicit water molecules in an implicit solvent calculation is necessary in order to accurately account for hydrogen bonding effects. Thiohydroxamic acids, like their hydroxamic acid analogues, are found to be N-acids, both in the gas phase and in aqueous solution.     

Study of baicalin scavenging hydroxyethyl peroxyl radicals by radiolysis of aerated ethanol-baicalin system

The reaction of baicalin (β- -glucopyranosiduronic acid, 5,6-dihydroxy-oxo-2-phenyl-4H-1-benzopyran-7-yl) scavenging hydroxyethyl peroxyl radicals (RO₂^.) was studied with the aid of radiolysis of aerated ethanol. Two main stable products were separated by reverse HPLC and their possible molecular structures were derived from their UV, IR and FAB-MS spectra. The dependence of G(H₂O₂), G(CH₃CHO) and G(-baicalin) on the concentration of baicalin showed that one baicalin molecule could inhibit the formation of one H₂O₂ molecule and two CH₃CHO molecules. A possible reaction mechanism between baicalin and RO₂^. radical was suggested.     

The role of chalcogen-chalcogen interactions in the intrinsic basicity acidity of beta-chalcogenovinyl(thio)aldehydes HC([double bond]X)[bond]CH[double bond]CH[bond]CYH

The intrinsic acidity and basicity of a series of beta-chalcogenovinyl(thio)aldehydes HC([double bond]X)[bond]CH[double bond]CH[bond]CYH (X=O, S; Y=Se, Te) were investigated by B3LYP/6-311+G(3df,2p) density functional and G2(MP2) calculations on geometries optimized at the B3LYP/6-31G(d) level for neutral molecules and at the B3LYP/6-31+G(d) level for anions. The results showed that selenovinylaldehyde and selenovinylthioaldehyde should behave as Se bases in the gas phase, because the most stable neutral conformer is stabilized by an X[bond]H...Se (X=O, S) intramolecular hydrogen bond (IHB). In contrast the Te-containing analogues behave as oxygen or sulfur bases, because the most stable conformer is stabilized by typical X...Y[bond]H chalcogen-chalcogen interactions. These compounds have a lower basicity than expected because either chalcogen-chalcogen interactions or IHBs become weaker upon protonation. Similarly, they are also weaker acids than expected because deprotonation results in a significantly destabilized anion. Loss of the proton from the X[bond]H or Y[bond]H groups is a much more favorable than from the C[bond]H groups. Therefore, for Se compounds the deprotonation process results in loss of the X[bond]H...Se (X=O, S) IHBs present in the most stable neutral conformer, while for Te-containing compounds the stabilizing X...Y[bond]H chalcogen-chalcogen interaction present in the most stable neutral conformer becomes repulsive in the corresponding anion.     

质子化和脱质子化对酞菁光谱的影响

系统地研究四异丙氧基酞菁的子化和脱质子化对吸收和发射光谱的影响，研究表明，三氟乙酸可对酞菁分子连续质子化，分别生成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．Ｈ＾＋）＾和（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．２Ｈ＾＋）＾２＋，而硫酸可使酞菁形成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．４Ｈ＾＋＾４＋此外，ＮａＯＨ／ＥｔＯＨ可使酞菁分子脱质子化生成（Ｐｃ（Ｏ＾ｉＰｒ）４）＾２－反应一步完成，表明分子中的两个吡咯－ＮＨ－同步酸解，质子化可使     

Superelectrophilic activation of 4-heterocyclohexanones. Implications for polymer synthesis. A theoretical study

The stability and the reactivity of mono- and diprotonated 4-heterocyclohexanones as well as cyclohexanone in triflic acid have been studied at the PBE0/aug-cc-pvtz//PBE0/6-31+G** level of theory. In all cases the first protonation is an exergonic process occurring at a carbonyl oxygen except for 4-piperidone where a nitrogen atom is protonated fist. Second protonation is only slightly endergonic for all studied molecules except for cyclohexanone where the second protonation is very unfavorable thermodynamically. According to calculations, diprotonated 4-heterocyclohexanones are much more active in the reactions of triflic acid mediated polyalkoxyalkylation with aromatic hydrocarbons compared to monoprotonated ones. The increase of the reactivity of diprotonated 4-heterocyclohexanones is due to inductive effect rather than through space electrostatic influence as follows from the electronic structure analysis of dications. Moreover, the second protonation reduces the possibility of an aldol condensation side reaction, reducing the enol electrophilicity rendering heterocyclohexanones as promising monomers for superacid mediated polyhydroxyalkylation.     

Cobalt complexes with tripodal ligands: implications for the design of drug chaperones

Extensive research is currently being conducted into metal complexes that can selectively deliver cytotoxins to hypoxic regions in tumours. The development of pharmacologically suitable agents requires an understanding of appropriate ligand-metal systems for chaperoning cytotoxins. In this study, cobalt complexes with tripodal tren (tris-(2-aminoethyl)amine) and tpa (tris-(2-pyridylmethyl)amine) ligands were prepared with ancillary hydroxamic acid, β-diketone and catechol ligands and several parameters, including: pK(a), reduction potential and cytotoxicity were investigated. Fluorescence studies demonstrated that only tpa complexes with β-diketones showed any reduction by ascorbate in situ and similarly, cellular cytotoxicity results demonstrated that ligation to cobalt masked the cytotoxicity of the ancillary groups in all complexes except the tpa diketone derivative [Co(naac)tpa](ClO(4))(2) (naac = 1-methyl-3-(2-naphthyl)propane-1,3-dione). Additionally, it was shown that the hydroxamic acid complexes could be isolated in both the hydroxamate and hydroximate form and the pK(a) values (5.3-8.5) reveal that the reversible protonation/deprotonation of the complexes occurs at physiologically relevant pHs. These results have clear implications for the future design of prodrugs using cobalt moieties as chaperones, providing a basis for the design of cobalt complexes that are both more readily reduced and more readily taken up by cells in hypoxic and acidic environments.     

Infrared spectroscopic studies of siderophore-related hydroxamic acid ligands adsorbed on titanium dioxide

The adhesion of bacteria to metal oxide and other mineral surfaces may involve bacterial siderophores, many of which contain hydroxamic acid (Ha) ligands. The adsorption behavior of the siderophore-related ligands acetohydroxamic acid, N-methylformohydroxamic acid, N-methylacetohydroxamic acid, and 1-hydroxy-2-piperidone on titanium dioxide thin films has been investigated using in situ ATR-IR spectroscopy with variation of concentration and pH. All the ligands were found to adsorb strongly on the TiO2 surface as hydroxamate ions and form bidentate surface complexes. Vibrational modes involving C=O stretching and N-O stretching of these ligands were assigned by comparing observed IR spectra with those calculated by the density functional method at the B3LYP/6-31+G(d) level. Calculated spectra of the complex [Ti(Ha)(OH)4]-, used to model the TiO2 surface, were compared with observed spectra of adsorbed hydroxamic acids. These results suggest that hydroxamic acid ligands in siderophores would be expected to bind to metal (oxide) and mineral surfaces during bacterial adhesion processes.