Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly_3,4NH₂ and Gly_3,4CysNH₂. The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (Δ_acid H) were determined to be 323.9 ± 2.5 kcal/mol (CysGly₃NH₂), 319.2 ± 2.3 kcal/mol (CysGly₄NH₂), 333.8 ± 2.1 kcal/mol (Gly₃CysNH₂), and 321.9 ± 2.8 kcal/mol (Gly₄CysNH₂), respectively. The corresponding deprotonation entropies (Δ_acid S) of the peptides were estimated. The gas-phase acidities (Δ_acid G) were derived to be 318.4 ± 2.5 kcal/mol (CysGly₃NH₂), 314.9 ± 2.3 kcal/mol (CysGly₄NH₂), 327.5 ± 2.1 kcal/mol (Gly₃CysNH₂), and 317.4 ± 2.8 kcal/mol (Gly₄CysNH₂), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31+G(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly_3,4(Cys-H)⁻NH₂, are also random coils. The two N-cysteine anionic peptides, (Cys-H)⁻Gly_3,4NH₂, may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly₃NH₂ and CysGly₄NH₂, are significantly more acidic than the corresponding C-terminal cysteine ones, Gly₃CysNH₂ and Gly₄CysNH₂. The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions.     

Gas-phase basicities of the isomeric dihydroxybenzoic acids and gas-phase acidities of their radical cations

The thermochemical acid/base properties of the six dihydroxybenzoic acids (x,y-DHB) as prototypical matrices used in matrix-assisted laser desorption/ionization (MALDI) have been investigated. The ground-state gas-phase basicities (GB) of the six DHB isomers and the gas-phase acidities (deltaG acid) of the corresponding radical cations ([x,y-DHB]*+) have been determined by Fourier-transform ion cyclotron resonance mass spectrometry employing the thermokinetic method. The gas-phase basicities vary from 814 kJ mol-1 for the least basic isomer, 3,5-DHB, to 831 kJ mol-1 for the most basic isomer, 2,4-DHB. The obtained gas-phase acidities of the corresponding radical cations vary from 815 kJ mol-1 for the most acidic species, 3,4-DHB, to 858 kJ mol-1 for the least acidic one, 2,5-DHB. The results indicate that ground-state proton transfer from the matrix radical cations to the analyte may play a role in the ionization process of MALDI, whereas proton transfer from protonated matrix molecules can be excluded.     

Gas-phase acidities of disubstituted methanes and of enols of carboxamides substituted by electron-withdrawing groups

The gas-phase acidities DeltaG degrees (acid) of some 20 amides/enols of amides RNHCOCHYY'/RNHC(OH)=CYY' [R = Ph, i-Pr; Y, Y' = CO(2)R', CO(2)R' ', or CN, CO(2)R', R', R' ' = Me, CH(2)CF(3), CH(CF(3))(2)], the N-Ph and N-Pr-i amides of Meldrum's acid, 1,3-cyclopentanedione, dimedone, and 1,3-indanedione, and some N-p-BrC(6)H(4) derivatives and of nine CH(2)YY' (Y, Y' = CN, CO(2)R', CO(2)R' '), including the cyclic carbon acids listed above, were determined by ICR. The acidities were calculated at the B3LYP/6-31+G//B3LYP/6-31+G level for both the enol and the amide species or for the carbon acid and the enol on the CO in the CH(2)YY' series. For 12 of the compounds, calculations were also conducted with the larger base sets 6-311+G and G-311+G. The DeltaG degrees (acid) values changed from 341.3 kcal/mol for CH(2)(CO(2)Me)(2) to 301.0 kcal/mol for PhNHC(OH)=C(CN)CH(CF(3))(2). The acidities increased for combinations of Y and Y' based on the order CO(2)Me < CO(2)CH(2)CF(3) < CN, CO(2)CH(CF(3))(2) for a single group and reflect the increased electron-withdrawal ability of Y,Y' coupled with the ability to achieve planarity of the crowded anion. The acidities of corresponding YY'-substituted systems follow the order N-Ph enols > N-Pr-i enols > CH(2)YY'. Better linear relationships between DeltaG degrees (acid) values calculated for the enols and the observed values than those for the values calculated for the amides suggest that the ionization site is the enolic O-H of most of the noncyclic trisubstituted methanes. The experimental DeltaG degrees (acid) value for Meldrum's acid matches the recently reported calculated value. The calculated structures and natural charges of all species are given, and the changes occurring in them on ionization are discussed. Correlations between the DeltaG degrees (acid) values and the pK(enol) values, which are linear for the trisubstituted methanes, excluding YY' = (CN)(2) and nonlinear for the CH(2)YY' systems, are discussed.     

Gas-phase hydrogen/deuterium exchange and conformations of deprotonated flavonoids and gas-phase acidities of flavonoids

Gas-phase hydrogen/deuterium (H/D) exchange was used to probe the conformations, gas-phase acidities, and sites of deprotonation of isomeric flavonoid aglycons and glycosides. The flavonoids in each isomer series were differentiated on the basis of their relative rate constants and total numbers of exchanges. For example, flavonoids that possess neohesperidose-type disaccharides may undergo faster and far more extensive exchange than isomeric rutinoside flavonoids. The structural factors that promote or prevent H/D exchange were identified and correlated with collisionally activated dissociation (CAD) patterns and/or molecular modeling data (both high-level ab initio acidity calculations and conformational analysis with molecular dynamics (MD) simulations), thus providing a framework for the use of H/D exchange reactions in the structural elucidation of new flavonoids.     

Gas-phase acidities and O-H bond dissociation enthalpies of phenol, 3-methylphenol, 2,4,6-trimethylphenol, and ethanoic acid

Energy-resolved, competitive threshold collision-induced dissociation (TCID) methods are used to measure the gas-phase acidities of phenol, 3-methylphenol, 2,4,6-trimethylphenol, and ethanoic acid relative to hydrogen cyanide, hydrogen sulfide, and the hydroperoxyl radical using guided ion beam tandem mass spectrometry. The gas-phase acidities of Delta(acid)H298(C6H5OH) = 1456 +/- 4 kJ/mol, Delta(acid)H298(3-CH3C6H4OH) = 1457 +/- 5 kJ/mol, Delta(acid)H298(2,4,6-(CH3)3C6H2OH) = 1456 +/- 4 kJ/mol, and Delta(acid)H298(CH3COOH) = 1457 +/- 6 kJ/mol are determined. The O-H bond dissociation enthalpy of D298(C6H5O-H) = 361 +/- 4 kJ/mol is derived using the previously published experimental electron affinity for C6H5O, and thermochemical values for the other species are reported. A comparison of the new TCID values with both experimental and theoretical values from the literature is presented.     

Equilibrium acidities of superacids

In this paper, we report the most comprehensive equilibrium superacidity scale that is available to date. Contrary to most of the past works, this scale is set up in a medium of constant composition and the obtained acidity values characterize the acidities of molecules rather than acidities of media. The current scale is thus complementary to the well-known H(0) scale in the information that it provides. The solvent used is 1,2-dichloroethane (DCE). DCE has very weak basic properties (but sufficiently high polarity) and is an appropriate solvent for measuring acidities of very strong acids of diverse chemical nature. DCE acidities of well-known superacids (CF(3)SO(2)OH, (CF(3)SO(2))(2)NH, cyanocarbon acids, etc.) as well as common mineral acids (H(2)SO(4), HI, HBr, etc.) are reported. Acidities of altogether 62 acids have been determined from 176 interlinked relative acidity measurements. The scale spans 15 orders of magnitude (from picric acid to 1,1,2,3,3-pentacyanopropene) and is expected to be a useful tool in design, use, and further acidity measurements of superacidic molecules.     

Vinyl hydrogen acidities of two stereoisomers

The gas-phase acidities of the vinyl hydrogens of cis- and trans-2-butene were measured by the silane kinetic method in a Fourier-transform ion cyclotron resonance spectrometer. The acidities of ethene and the secondary vinyl hydrogen of propene were measured by the same method. The method was calibrated using the known acidities of methane and benzene. The vinyl hydrogens of trans-2-butene are more acidic than the vinyl hydrogens of cis-2-butene by 4.5 kcal/mol; the acidities of ethene and the secondary vinyl hydrogen of propene are between those of the two butenes. The acidity of cis-2-butene is 409 +/- 2 kcal/mol, and the acidity of trans-2-butene is 405 +/- 2 kcal/mol. Density functional theory calculations are in good agreement with the experiments. The results are discussed in terms of steric interactions, polarizabilities, dipole-dipole interactions, and charge-dipole interactions.     

Semi-empirical all-valence-electron SCF calculations of acidities of cycloalkanes

CNDO/2 calculations of the energy change RHR^–+H⁺ for cycloalkanes give the acidity order: cyclohexane > cyclopentane > cyclobutane > cyclopropane, exactly the reverse of the experimental order. INDO results are similar to CNDO/2. A new method, IRDO, related to NDDO is described. Both of these methods give results differing from the first two but agreement with experiment is still poor.

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Zusammenfassung CNDO/2-Berechnungen der Energieänderung der Reaktion RHR^–+H⁺ für Cycloalkane gibt folgende Reihenfolge für die Acidität: Cyclohexan > Cyclopentan > Cyclobutan > Cyclopropan, was genau der umgekehrten experimentellen Reihenfolge entspricht. INDO Resultate sind den CNDO/2 Resultaten ähnlich. Eine neue Methode, IRDO, die der NDDO verwandt ist, wird vorgeschlagen. Diese Methoden führen zu Resultaten, die sich von denen der beiden ersten unterscheiden, aber die Übereinstimmung mit dem Experiment ist noch immer unbefriedigend.

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Résumé Des calculs CNDO/2 de la variation d'énergie de la réaction RHR^–+H⁺ pour les cycloalkanes donnent l'ordre des acidités à l'inverse de l'ordre experimental: cyclohexane > cyclopentane > cyclobutane > cyclopropane. Les résultats INDO sont semblables à ceux de CNDO/2. Une nouvelle méthode, IRDO, liée à NDDO est décrite. Ces deux méthodes donnent des résultats différents des deux premières, mais l'accord avec l'expérience reste faible.

     

Cyclopropenium-activated cyclodehydration of diols

The dehydrative cyclization of diols to cyclic ethers via cyclopropenium activation is described. Using 2,3-diphenylcyclopropene and methanesulfonic anhydride, a series of 1,4- and 1,5-diols are rapidly cyclized to furnish tetrahydrofurans and tetrahydropyrans in high yield. Eleven total substrates are shown, including a gram scale cyclization of a diterpene derivative.     

Electronic absorption spectra and acidities of heteroaromatic thiols

The electronic absorption spectra of a number of substituted and unsubstituted thiophene-, benzothiophene-, and benzofuranthiols were studied, and their ionization constants were determined by establishment of the dependence of the optical densities of aqueous alcohol solutions of them on the pH.Translated from Khimiya Getero-tsiklicheskikh Soedinenii, No. 10, pp. 1313–1314, October, 1980.     

Gas-phase basicity of methionine

Proton affinity and protonation entropy of methionine (Met) were determined by the extended kinetic method from ESI-Q-TOF tandem mass spectrometry experiments. The values, PA(Met) = 937.5 +/- 2.9 kJ mol(-1) and Delta(p)S degrees (Met) = - 22 +/- 5 J mol(-1) K(-1), lead to gas-phase basicity GB(Met) = 898.2 +/- 3.2 kJ.mol(-1). Quantum chemical calculations using density functional theory confirm that the proton affinity of Met is indeed in the 940 kJ mol(-1) range and that a significant entropy loss, of at least - 25 J mol(-1) K(-1), occurs upon protonation. This last point is evidenced here for the first time and suggests revision of the tabulated protonation thermochemistry of Met. A comparison with previous experimental data allows us to propose the following evaluated thermochemical values: PA(Met) = 943 +/- 4 kJ mol(-1) and Delta(p)S degrees (Met) = - 35 +/- 15 J mol(-1) K(-1) and GB(Met) = 900 +/- 2 kJ mol(-1).     

Gas-phase basicities of polyamines

The gas-phase basicities of a group of multidentate polyamines have been determined by the bracketing method and range from 966 to 1021 kJ/mol. The compounds studied vary in the number and kind of basic sites, the number and orientation of carbon atoms, and the degree of flexibility. These important structural features were analyzed to understand the observed trends in basicity and semiempirical calculations were undertaken that support the experimental trends. The polyamines may find use as reference compounds for future gas-phase basicity measurements of larger, biologically active molecules such as peptides and proteins.     

First-principle calculation of equilibrium cesium ion-pair acidities in tetrahydrofuran

The ion-pair acidities of organic acids in THF are fundamental to synthetic organic chemistry. Although the ion-pair acidities of a number of carbon acids have been experimentally measured by Streitwieser and co-workers, it is important to develop a theoretical method that can accurately predict these quantities because not all the organic acids (e.g., very weak acids or complex synthetic intermediates with multiple acidic positions) are amenable to experimental characterization. In the present study is reported the first theoretical protocol for predicting the cesium ion-pair acidities in THF whose reliability has been tested against almost all the available experimental data. It is found that the root-mean-square error of the current theoretical model equals 1.2 pK units. With the newly developed theoretical method in hand, the structures of cesium ion pairs of different types of carbon acids are then studied. The cesium ion-pair acidities in THF and absolute ionic acidities in DMSO are also systematically compared, which confirms Streitwieser's previous finding that the two scales of acidities have only minor difference. Significantly, from detailed energy analysis the mechanism for the "fortunate" match of the two scales of acidities is found. That is, the combined process of the Cs binding ("micro"-solvation) and the solvation of the ion pair resembles the one-step solvation of a carbanion in DMSO. Finally, it is found that the cesium ion-pair acidities of nitrogen acids in THF have only minor difference from the absolute ionic acidities in DMSO. Consequently, one can easily estimate the cesium ion-pair acidities of almost all types of organic nitrogen acids in THF on the basis of Bordwell's data.     

Effect of phosphoryl and thiophosphoryl groups on CH acidities

It is shown that the CH acidities of phosphoryl and thiophosphoryl compounds depend on the substituents attached to both the carbon atom and the phosphorus atom and comply with Hammett dependences; the parameters of the correlation dependences are very close for the two types of compounds, and this makes it possible to propose a general equation for calculating the pK values of CH acids that contain a phosphoryl or thiophosphoryl group.A. N. Nesmeyanov Institute of Heteroorganic Compounds, Academy of Sciences of the USSR, Moscow. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 27, No. 3, pp. 284–288, May–June, 1991. Original article submitted February 18, 1991.