Superoxide radical anion adduct of 5,5-dimethyl-1-pyrroline n-oxide (DMPO). 1. The thermodynamics of formation and its acidity

The nitrone 5,5-dimethyl-1-pyrroline N-oxide (DMPO) has been the most widely used spin trap for the detection of transient free radicals in chemical, biological, and biomedical research using electron paramagnetic resonance (EPR) spectroscopy. A density functional theory (DFT) approach was used to predict the thermodynamics of formation of the superoxide anion/hydroperoxyl radical (O2*-/*O2H) adduct of DMPO as well as its pK(a) in aqueous systems. At the B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) level, we predicted (in the gas phase and with a polarizable continuum model (PCM) for water) three conformational minima for both the DMPO-O2- and DMPO-O2H adducts. Using DFT and the PCM solvation method, the pK(a) of DMPO-O2H was predicted to be 14.9 +/- 0.5. On the basis of free energy considerations, the formation of DMPO-O2H at neutral pH proceeds via initial addition of O2*- to DMPO to form the DMPO-O2- adduct and then subsequent protonation by water (or other acidic sources) to form DMPO-O2H. Under acidic conditions, the addition of *O2H to DMPO is predicted to be more exoergic than the addition of O2*- and is consistent with available experimental kinetic data.     

Theoretical and experimental studies of the spin trapping of inorganic radicals by 5,5-dimethyl-1-pyrroline N-oxide (DMPO). 1. Carbon dioxide radical anion

The carbon dioxide radical anion (CO2*-) is known to be generated in vivo through various chemical and biochemical pathways. Electron paramagnetic resonance (EPR) spin trapping with the commonly used spin trap, 5,5-dimethyl-1-pyrroline N-oxide (DMPO), has been employed in the detection of CO2*-. The thermodynamics of CO2*- addition to DMPO was predicted using density functional theory (DFT) at the B3LYP/6-31++G**//B3LYP/6-31G* and B3LYP/6-311+G* levels with the polarizable continuum model (PCM) to simulate the effect of the bulk dielectric effect of water on the calculated energetics. Three possible products of CO2*- addition to DMPO were predicted: (1) a carboxylate adduct, (2) pyrroline-alcohol and (3) DMPO-OH. Experimentally, UV photolysis of H2O2 in the presence of sodium formate (NaHCO2) and DMPO gave an EPR spectrum characteristic of a C-centered carboxylate adduct and is consistent with the theoretically derived hyperfine coupling constants (hfcc). The pKa of the carboxylate adduct was estimated computationally to be 6.4. The mode of CO2*- addition to DMPO is predicted to be governed predominantly by the spin (density) population on the radical, whereas electrostatic effects are not the dominant factor for the formation of the persistent adduct. The thermodynamic behavior of CO2*- in the aqueous phase is predicted to be similar to that of mercapto radical (*SH), indicating that formation of CO2*- in biological systems may have an important role in the initiation of oxidative damage in cells.     

Theoretical and experimental studies of the spin trapping of inorganic radicals by 5,5-dimethyl-1-pyrroline N-oxide (DMPO). 2. Carbonate radical anion

Previous studies have shown that the enzyme-mediated generation of carbonate radical anion (CO(3)(.-)) may play an important role in the initiation of oxidative damage in cells. This study explored the thermodynamics of CO(3)(.-) addition to 5,5-dimethyl-1-pyrroline N-oxide (DMPO) using density functional theory at the B3LYP/6-31+G(**)//B3LYP/6-31G* and B3LYP/6-311+G* levels with the polarizable continuum model to simulate the effect of the bulk dielectric effect of water on the calculated energetics. Theoretical data reveal that the addition of CO(3)(.-) to DMPO yields an O-centered radical adduct (DMPO-OCO2) as governed by the spin (density) population on the CO(3)(.-). Electron paramagnetic resonance spin trapping with the commonly used spin trap, DMPO, has been employed in the detection of CO(3)(.-). UV photolysis of H(2)O(2) and DMPO in the presence of sodium carbonate (Na(2)CO(3)) or sodium bicarbonate (NaHCO(3)) gave two species (i.e., DMPO-OCO(2) and DMPO-OH) in which the former has hyperfine splitting constant values of a(N) = 14.32 G, a(beta)-Eta = 10.68 G, and a(gamma-H) = 1.37 G and with a shorter half-life compared to DMPO-OH. The origin of the DMPO-OH formed was experimentally confirmed using isotopically enriched H(2)(17)O(2) that indicates direct addition of HO(.) to DMPO. Theoretical studies on other possible pathways for the formation of DMPO-OH from DMPO-OCO(2) in aqueous solution and in the absence of free HO(.) such as in the case of enzymatically generated CO(3)(.-), show that the preferred pathway is via nucleophilc substitution of the carbonate moiety by H(2)O or HO(-). Nitrite formation has been observed as the end product of CO(3)(.-) trapping by DMPO and is partly dependent on the basicity of solution. The thermodynamic behavior of CO(3)(.-) in the aqueous phase is predicted to be similar to that of the hydroperoxyl (HO(2)(.)) radical.     

Theoretical study of the spin trapping of hydroxyl radical by cyclic nitrones: a density functional theory approach

The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.     

Theoretical and experimental studies of the spin trapping of inorganic radicals by 5,5-dimethyl-1-pyrroline N-oxide (DMPO). 3. Sulfur dioxide, sulfite, and sulfate radical anions

Radical forms of sulfur dioxide (SO(2)), sulfite (SO(3)(2-)), sulfate (SO(4)(2-)), and their conjugate acids are known to be generated in vivo through various chemical and biochemical pathways. Oxides of sulfur are environmentally pervasive compounds and are associated with a number of health problems. There is growing evidence that their toxicity may be mediated by their radical forms. Electron paramagnetic resonance (EPR) spin trapping using the commonly used spin trap, 5,5-dimethyl-1-pyrroline N-oxide (DMPO), has been employed in the detection of SO(3)(?-) and SO(4)(?-). The thermochemistries of SO(2)(?-), SO(3)(?-), SO(4)(?-), and their respective conjugate acids addition to DMPO were predicted using density functional theory (DFT) at the PCM/B3LYP/6-31+G**//B3LYP/6-31G* level. No spin adduct was observed for SO(2)(?-) by EPR, but an S-centered adduct was observed for SO(3)(?-)and an O-centered adduct for SO(4)(?-). Determination of adducts as S- or O-centered was made via comparison based on qualitative trends of experimental hfcc's with theoretical values. The thermodynamics of the nonradical addition of SO(3)(2-) and HSO(3)(-) to DMPO followed by conversion to the corresponding radical adduct via the Forrester-Hepburn mechanism was also calculated. Adduct acidities and decomposition pathways were investigated as well, including an EPR experiment using H(2)(17)O to determine the site of hydrolysis of O-centered adducts. The mode of radical addition to DMPO is predicted to be governed by several factors, including spin population density, and geometries stabilized by hydrogen bonds. The thermodynamic data supports evidence for the radical addition pathway over the nucleophilic addition mechanism.     

4-Aryl-1,3,2-oxathiazolylium-5-olates as pH-controlled NO-donors: the next generation of S-nitrosothiols

S-Nitrosothiols (RSNOs) are important exogenous and endogenous sources of nitric oxide (NO) in biological systems. A series of 4-aryl-1,3,2-oxathiazolylium-5-olates derivatives with varying aryl para-substituents (-CF3, -H, -Cl, and -OCH3) were synthesized. These compounds were found to release NO under acidic condition (pH = 5). The decomposition pathway of the aryloxathiazolyliumolates proceeded via an acid-catalyzed ring-opening mechanism after which NO was released and an S-centered radical was generated. Electron paramagnetic resonance (EPR) spin trapping studies were performed to detect NO and the S-centered radical using the spin traps of iron(II) N-methyl-D-glucamine dithiocarbamate [(MGD)2-FeII] and 5,5-dimethyl-1-pyrroline N-oxide (DMPO). Also, EPR spin trapping and UV-vis spectrophotometry were used to analyze the effect of aryl para substitution on the NO-releasing property of aryloxathiazolyliumolates. The results showed that the presence of an electron-withdrawing substituent such as -CF3 enhanced the NO-releasing capability of the aryloxathiazolyliumolates, whereas an electron-donating substituent like methoxy (-OCH3) diminished it. Computational studies using density functional theory (DFT) at the PCM/B3LYP/6-31+G**//B3LYP/6-31G* level were used to rationalize the experimental observations. The aryloxathiazolyliumolates diminished susceptibility to reduction by ascorbate or gluthathione, and their capacity to cause vasodilation as compared to other S-nitrosothiols suggests potential application in biological systems.     

Comparative DFT study of the spin trapping of methyl, mercapto, hydroperoxy, superoxide, and nitric oxide radicals by various substituted cyclic nitrones

The thermodynamics of the spin trapping of various cyclic nitrones with biologically relevant radicals such as methyl, mercapto, hydroperoxy, superoxide anion, and nitric oxide was investigated using computational methods. A density functional theory (DFT) approach was employed in this study at the B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) level. The order of increasing favorability for Delta G(rxn) (kcal/mol) of the radical reaction with various nitrones, in general, follows a trend similar to their respective experimental reduction potentials as well as their experimental second-order rate constants in aqueous solution: NO (14.57) < O2*- (-7.51) < *O2H (-13.92) < *SH (-16.55) < *CH3 (-32.17) < *OH (-43.66). The same qualitative trend is predicted upon considering the effect of solvation using the polarizable continuum model (PCM): i.e., NO (14.12) < O2*- (9.95) < *O2H (-6.95) < *SH (-13.57) < *CH3 (-32.88) < *OH (-38.91). All radical reactions with these nitrones are exoergic, except for NO (and O2*- in the aqueous phase), which is endoergic, and the free energy of activation (Delta G) for the NO additions ranges from 17.7 to 20.3 kcal/mol. This study also predicts the favorable formation of certain adducts that exhibit intramolecular H-bonding interactions, nucleophilic addition, or H-atom transfer reactions. The spin density on the nitronyl N of the superoxide adducts reveals conformational dependences. The failure of nitrones to trap NO at normal conditions was theoretically rationalized due to the endoergic reaction parameters.     

双氮桥联1,10-菲咯啉大环化合物分子构型的从头算研究

应用规范不变原子轨道法(GIAO)在RHF/6-31G**和B3LYP/6-31G**水平上计算了质子化双氮桥联1,10-菲咯啉大环化合物(H4HAPP2+)C2h和C2h构型的1HNMR,并用TDDFT法计算了H4HAPP2+电子光谱.结果表明,B3LYP/6-31G*优化的C2h构型为较优构型,经谐振频率验证无虚频,C2h构型是H4HAPP2+合理的对称性构型.     

Reactivity of superoxide radical anion with cyclic nitrones: role of intramolecular H-bond and electrostatic effects

Limitations exist among the commonly used cyclic nitrone spin traps for biological free radical detection using electron paramagnetic resonance (EPR) spectroscopy. The design of new spin traps for biological free radical detection and identification using EPR spectroscopy has been a major challenge due to the lack of systematic and rational approaches to their design. In this work, density functional theory (DFT) calculations and stopped-flow kinetics were employed to predict the reactivity of functionalized spin traps with superoxide radical anion (O2*-). Functional groups provide versatility and can potentially improve spin-trap reactivity, adduct stability, and target specificity. The effect of functional group substitution at the C-5 position of pyrroline N-oxides on spin-trap reactivity toward O2*- was computationally rationalized at the PCM/B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) and PCM/mPW1K/6-31+G(d,p) levels of theory. Calculated free energies and rate constants for the reactivity of O2*- with model nitrones were found to correlate with the experimentally obtained rate constants using stopped-flow and EPR spectroscopic methods. New insights into the nucleophilic nature of O2*- addition to nitrones as well as the role of intramolecular hydrogen bonding of O2*- in facilitating this reaction are discussed. This study shows that using an N-monoalkylsubstituted amide or an ester as attached groups on the nitrone can be ideal in molecular tethering for improved spin-trapping properties and could pave the way for improved in vivo radical detection at the site of superoxide formation.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid

2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-mercaptopropanoic acid

2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.     

1-Azabicyclo[3.3.1]nonan-2-one: nitrogen versus oxygen protonation

Protonation of typical unstrained amides and lactams is heavily favored at oxygen. In contrast, protonation of the highly distorted lactam 1-azabicyclo[2.2.2]octan-2-one is heavily favored at nitrogen. What structures occupy "crossover boundaries" where N- and O-protonation are nearly equienergetic? Density function theory calculations at the B3LYP/6-31G* level, as well as QCISD(T)/6-31G* calculations, predict that 1-azabicyclo[3.3.1]nonan-2-one favors N-protonation at nitrogen only very slightly (<2.0 kcal/mol; "gas phase") over O-protonation. (1)H and (13)C NMR as well as ultraviolet (UV) studies of this lactam, in its combination with sulfuric acid, confirm predominant protonation at nitrogen. Although the calculations very slightly favor the N-protonated chair-chair conformation, experimental spectra clearly support the N-protonated boat-chair. Broadened resonances in the (13)C NMR spectrum suggest an exchange phenomenon. Variable-temperature studies of the (13)C NMR spectra support dynamic exchange between the major tautomer (N-protonated) and the minor tautomer (O-protonated) in a roughly 4:1 mixture. The findings also support the published prediction that a twisted bridgehead lactam with the nitrogen lone pair (n(N)) as HOMO will protonate at nitrogen.     

Spectroscopic, quantum chemical DFT/HF study and synthesis of [2.2.1] hept-2'-en-2'-amino-N-azatricyclo [3.2.1.0(2,4)] octane

The compound 4-N-bicyclo [2.2.1] hept-2'-en-2'-amino-N-azatricyclo [3.2.1.0(2,4)] octane (2) has been synthesized and characterized by elemental analysis, IR, UV-vis, mass and NMR. Density functional theory (DFT) and Hartree-Fock (HF) calculations have been carried out for the title compound by using the standard 6-31G* basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they complement each other. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT and ZINDO methods. The (13)C NMR and (1)H NMR of compound (2) have been calculated by means of Becke 3-Lee-Yang-Parr (B3LYP) density functional method with 6-31G* basis set. Comparison between the experimental and the theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated.     

Quantum chemistry-based NMR spin Hamiltonian parameters of GABA for quantitation in magnetic resonance spectroscopy

Chemical shifts delta and spin-spin coupling constants J have been calculated using quantum chemistry approaches for the gamma-amino butyric acid GABA which is a brain metabolite. Two theoretical methods HF and DFT/B3LYP, two basis sets 6-31G* and 6-311+G(2d,p) and two gauge-invariant methods CSGT and GIAO have been used. From delta and J values, NMR spectra have been obtained from the strongly coupled spin system Hamiltonian using the NMR-SCOPE package. Solvent effects have been considered within the polarisable continuum model. Comparisons between calculated and experimental NMR spectra at 300 MHz show that our best results correspond to the B3LYP/6-311+G(2d,p)-GIAO calculations. They are seen to be in good agreement with experiment. This demonstrates the usefulness of quantum chemistry methods for estimating NMR spin Hamiltonian parameters involved in specific algorithms used for quantitation of metabolites such as GABA.     

2-丁基-四氢噻吩亚砜13C-NMR的理论研究

在RHF/6-31G和B3LYP/6-31G水平上对顺式(Cis-)与反式(Trans-)2-丁基-四氢噻吩亚砜(BTHTO)进行几何优化,应用规范不变原子轨道法(GIAO)在6-31G、6-31+G、6-31++G和6-31+G(2d,p)水平上计算了Cis-和Trans-BTHTO的13C-NMR,对13C-NMR谱进行了归属。结果表明,BTHTO噻吩五元环的稳定构象呈半椅式,Cis-和Trans-BTHTO中与硫原子直接碳原子13C-NMR的显著差异主要是由于空间构型不同引起分子的静电势场对相应碳原子的屏蔽作用不同所致。     

Iminopropadienones R–NCCCO and carbon suboxide, C3O2. Theoretical and experimental C NMR spectra

The ¹³C NMR data of five iminopropadienones R–NCCCO as well as carbon suboxide, C₃O₂, have been examined theoretically and experimentally. The best theoretical results were obtained using the GIAO/B3LYP/6-31+G**//MP2/6-31G* level of theory, which reproduces the chemical shifts of the iminopropadienone substituents extremely well while underestimating those of the cumulenic carbons by 5–10 ppm. The computationally faster GIAO/HF/6-31+G**//B3LYP/6-31G* level is also adequate.     

Synthesis,Characterization and Theoretical Studies on a Thiocarbamide Derivative Containing Schiff Base Group

A thiocarbamide derivative containing Schiff base groups,1,5-bis[4-(dimethylamino)benzylidene]thiocarbonohydrazide,has been synthesized and characterized by elemental analysis,IR,1H NMR,UV and X-ray single-crystal diffraction.Density function theory(DFT) calculations at the B3LYP/6-31G* and PBE0/6-31G* levels for optimized geometries and electronic transition spectra have been performed.Comparative studies show that both B3LYP/6-31G* and PBE0/6-31G* methods can well reproduce the molecular structure,and the latter is more reliable than the former to simulate electronic spectra.NPA calculational results at the B3LYP/6-31G* level indicate the title compound to be a potential multidentate ligand to the metallic ions.Based on the vibrational analysis,thermodynamic properties at different temperatures have been obtained.     

FC(O)NCS 分子振动光谱的理论研究

采用DFT(B3LYP)方法,以6-3G*为基组对FC(O)NCS的顺式和反式两种构型的几何结构,振动谐性力场和红外光谱进行了研究。B3LYP/6-31G*计算水平和大多数有机分子的一套固定标度因子进行标度。根据标度后的理论力场进行简正坐标分析得到的势能分布(PED)和红外光谱强度值对FC(O)NCS分子的顺式和反式两种构型的振动基频进行了理论归属。     

First example of conformational exchange in a natural taxane enolate

A detailed NMR study and full assignments of the (1)H- and (13)C-NMR spectral data for a novel enolate taxane isolated from Taxus canadensis needles is described. The structures of two stable conformers were established using a combination of 1D and 2D NMR techniques including (1)H, (1)H-COSY, gs-HMQC, gs-HMBC, NOESY and T-ROESY. Ab initio quantum mechanical calculations were performed on the B3LYP/6-31G* level of basis set to assist the NMR findings.     

Rate constants of hydroperoxyl radical addition to cyclic nitrones: a DFT study

Nitrones are potential synthetic antioxidants against the reduction of radical-mediated oxidative damage in cells and as analytical reagents for the identification of HO2* and other such transient species. In this work, the PCM/B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) and PCM/mPW1K/6-31+G(d,p) density functional theory (DFT) methods were employed to predict the reactivity of HO2* with various functionalized nitrones as spin traps. The calculated second-order rate constants and free energies of reaction at both levels of theory were in the range of 100-103 M-1 s-1 and 1 to -12 kcal mol-1, respectively, and the rate constants for some nitrones are on the same order of magnitude as those observed experimentally. The trend in HO2* reactivity to nitrones could not be explained solely on the basis of the relationship of the theoretical positive charge densities on the nitronyl-C, with their respective ionization potentials, electron affinities, rate constants, or free energies of reaction. However, various modes of intramolecular H-bonding interaction were observed at the transition state (TS) structures of HO2* addition to nitrones. The presence of intramolecular H-bonding interactions in the transition states were predicted and may play a significant role toward a facile addition of HO2* to nitrones. In general, HO2* addition to ethoxycarbonyl- and spirolactam-substituted nitrones, as well as those nitrones without electron-withdrawing substituents, such as 5,5-dimethyl-pyrroline N-oxide (DMPO) and 5-spirocyclopentyl-pyrroline N-oxide (CPPO), are most preferred compared to the methylcarbamoyl-substituted nitrones. This study suggests that the use of specific spin traps for efficient trapping of HO2* could pave the way toward improved radical detection and antioxidant protection.