The kinetic method reveals secondary deuterium isotope effects on the proton affinity and gas-phase basicity of glycine and alanine methyl esters

The kinetic method for measuring proton affinities (PA) and gas-phase basicities (GB) was applied to the methyl esters of simple amino acids. The experiments show that the GB and PA values for deuterium labeled glycine methyl ester are indeed greater than that of the corresponding unlabelled glycine methyl ester. The PA of -Ala-OCD₃ is also slightly greater than that of the unlabeled alanine methyl ester. The secondary isotope effects originate, as shown by density functional theory, in differences in zero-point energies and thermal-energy corrections between H and D-bearing molecules.     

Proton affinities and relative basicities of two 1,4,7-triazacyclononanes, Me3TACN and TP-TACN. Quantum-chemical ab initio calculations, solution measurements, and the structure of [TP-TACN·2H] in the solid state

Quantum-chemical ab initio calculations have been carried out to determine the proton affinities of tripyrollidinyl- and 1,4,7-trimethyl-1,4,7-triazacyclononane. Due to an effective stabilization of the ammonium cations the proton affinities of both compounds have been found to be up to 20 kcal/mol higher than the values of non-cyclic tertiary aliphatic amines. The computational results have been compared to those from solution measurements and X-ray structure determination.     

Proton affinities of molecules containing nitrogen and oxygen: Comparing density functional results to experiment

Summary Proton affinities were calculated using density functional theory for 11 small molecules whose primary protonation site is on nitrogen, and eight small molecules that protonate on oxygen. Calculations were performed using both the local spin density approximation and nonlocal gradient corrections to the exchange correlation functional. The results were not sensitive to whether the nonlocal gradient correction was implemented on the final local spin density optimized geometry or whether the correction was included in the self-consistent calculation of the energy at each optimization step. Although negligible basis set dependence was found using the analytic Gaussian basis sets, numerical basis sets required augmentation by a double set of polarization functions to achieve reasonable agreement with experiment. All calculations systematically underestimated oxygen proton affinities.     

Calculation of the enthalpies of formation and proton affinities of some isoquinoline derivatives

Ab initio molecular orbital theory has been used to calculate enthalpies of formation of isoquinoline, 1-hydroxyisoquinoline, 5-hydroxyisoquinoline, and 1,5-dihydroxyisoquinoline as well as some pyridine and quinoline derivatives. The proton affinities of the four isoquinoline derivatives were also obtained. The high-level composite methods G3(MP2), G3(MP2)//B3LYP, G3//B3LYP, and CBS-QB3 have been used for this study, and the results have been compared with available experimental values. For six of the eight studied compounds, the theoretical enthalpies of formation were very close to the experimental values (to within 4.3 kJ · mol⁻¹); where comparison was possible, the theoretical and experimental proton affinities were also in excellent agreement with one another. However, there is an extraordinary discrepancy between theory and experiment for the enthalpies of formation of 1-hydroxyisoquinoline and 1,5-dihydroxyisoquinoline, suggesting that the experimental values for these two compounds should perhaps be re-examined. We also show that popular low cost computational methods such as B3LYP and MP2 show very large deviations from the benchmark values.     

DFT,CBS‐Q,W1BD and G4MP2 calculation of the proton and electron affinities,gas phase basicities and ionization energies of saturated and unsaturated carboxylic acids (C1–C4)

The proton affinities, gas phase basicities and ionization energies of formic acid, acetic acid, propanoic acid, 2‐propenoic acid, propiolic acid, butanoic acid, 2‐butenoic acid, 3‐botenoic acid, 2‐methyl‐propanoic acid and 2‐methyl‐2‐propenoic acid were calculated using the computational methods including B3LYP/6‐311++G(2df,p), CBS‐Q and G4MP2. Also, the considered properties were calculated using W1BD method only for formic and acetic acids. In addition, the electron affinities of the acids were calculated using B3LYP, CBS‐Q, G4MP2 and G2MP2 methods, separately. The calculations showed that the PA and gas phase basicity increase with the increase in the number of carbon atoms. The calculated Ionization energies of the unsaturated carboxylic acids are less than the corresponding saturated acids, which are in good agreement with the experimental results. © 2013 Wiley Periodicals, Inc.     

The proton affinities and proton transfer in imine, amidine and guanidine series

The enthalpies of formation of neutral and protonated alkyl imines, amidine and guanidine are obtained by ab initio theoretical means using an isodesmic reaction technique. The corresponding proton affinities are obtained and discussed in terms of thermochemical stabilization energies. Their relation to the proton transfer process is examined and discussed. To this end, the structure and properties of various molecular complexes obtained between these molecules of interest and formic acid are explored. The sensitivity of this process to the presence of a neighbour water molecule is commented.     

Structures, vibrational frequencies, and electron affinities of SF5On/SF5On (n = 1–3)

The molecular structures, vibrational frequencies, and electron affinities of the SF₅O_n/SF₅O_n⁻ (n = 1–3) species have been examined with four hybrid density functional theory (DFT) methods. The basis set used in this work is of double-ζ plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. The SF₅O_n (n = 1–3) species should be potential greenhouse gases. The anion SF₅O₂⁻ with C_s symmetry has a ³A″ electronic state, and the neutral SF₅O₃ with ²A″ electronic state has C_s symmetry. The anions SF₅O₂⁻ and SF₅O₃⁻ should be regarded as SF₅⁻·O₂ and SF₅O⁻·O₂ complexes, respectively. Three different types of the neutral–anion energy separation presented in this work are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). The EA_ad values predicted by the B3PW91 method are 5.22 (SF₅O), 4.38 (SF₅O₂), and 3.61 eV (SF₅O₃). Compared with the experimental vibrational frequencies, the BHLYP method overestimates the frequencies, and the other three methods underestimate the frequencies. The bond dissociation energies D_e (SF₅O_n → SF₅O_n−m + O_m) for the neutrals SF₅O_n and D_e (SF₅O_n⁻ → SF₅O_n−m⁻ + O_m and SF₅O_n⁻ → SF₅O_n−m + O_m⁻) for the anions SF₅O_n⁻ are reported.     

The unimolecular chemistry of protonated glycine and the proton affinity of glycine: a computational model

The potential energy hypersurface of protonated glycine, GH⁺, has been investigated. The calculated G2(MP2) value for the proton affinity (PA) of glycine, PA _calc=895kJ mol⁻¹, is in good agreement with the experimental value which has been estimated to lie in the range 864kJ mol⁻¹ < PA _exp <891kJ mol⁻¹. Ab initio quantum chemical calculations of relevant parts of the potential energy surface of GH⁺ give a reaction model which is consistent with the observed mass spectrometric fragmentation pattern. The lowest energy unimolecular reactions of GH⁺ are two distinct processes: (1) loss of CO, which has a substantial barrier for the reverse reaction, and (2) loss of CO plus H₂O, which has no barrier for the reverse reaction. Received: 15 November 1996 / Accepted: 6 May 1997     

Chiral superbases: the proton affinities of 1- and 2-aza[6]helicene in the gas phase

The proton affinities (PAs) of 1- and 2-azahelicene were determined using various mass spectrometric techniques and complementary results from density functional theory. With PAs of about 1000 kJ mol(-1), the helical backbone of both compounds offer promising perspectives for future research on enantioselective reactions of these helical nitrogen bases.     

Understanding selenocysteine through conformational analysis,proton affinities,acidities and bond dissociation energies

Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6‐31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6‐311++G*//B3LYP/6‐31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Peptide models II. Intramolecular interactions and stable conformations of glycine,alanine, and valine peptide analogues

Summary The stable conformations of N and C protected amino acids of the type: HCONH-CHR-CONH₂ of glycine,l-alanine andl-valine have been obtained by fully optimizedab-initio computations with a 3–21G basis set. An original procedure has been devised to extract the side-chain/backbone interaction energy and the backbone and side-chain distortion energies. This enables us to analyze the stabilization/destabilization effects introduced by the side-chain in terms of electrostatic, induction and steric hindrance contributions.Dedicated to Dr. A. Pullman     

Gas phase acidities of CH bonds adjacent to oxygen and to sulphur

It has been shown, by double zeta quality ab initio MO calculations, that, in the gas phase, a CH bond adjacent to sulphur is more acidic than a CH bond adjacent to oxygen. This trend is in agreement with experimental observations in solution.     

核酸碱基互变异构体的结构、稳定性及其物理化学性质

核酸碱基是DNA及RNA分子的重要组成部分, 在基因遗传信息的传递方面起着主导作用. 核酸碱基存在多种互变异构体, 它们在DNA及RNA分子中主要以最稳定的异构体形式存在, 但是在气相或凝聚相中也有少量的其他异构体形式存在. 核酸碱基的稀有互变异构体往往能够引起碱基对的错配对, 这可能会导致DNA及RNA分子形成不规则的结构, 并进一步导致DNA或RNA双螺旋的自发突变. 因此, 对核酸碱基的互变异构体进行系统的研究, 有助于人们深入认识DNA和RNA分子的结构和性质. 国际上有很多研究小组已经通过实验和理论对核酸碱基互变异构体的结构、相对能量及其性质进行了研究. 本文对文献中有关核酸碱基互变异构体的实验和理论研究进行了综述. 在对前人研究进行归纳总结的基础上, 我们利用密度泛函计算对核酸碱基的互变异构体进行了排序, 得到的最优异构体结构参数和相对能量与实验值相比较为一致. 此外, 因为核酸碱基的物理化学性质可以为生物、化学、材料等方面的研究提供重要的基础性信息, 因此我们还对它们的电子亲和能、电离能、质子亲和能等研究进行了总结.     

Structures, electron affinities, and vibrational frequencies of the mono-, di-substituted SF6 radicals

Optimized molecular structures, electron affinities, and IR-active vibrational frequencies have been predicted using five different hybrid Hartree–Fock/density functional theory (DFT) methods for a series of mono-, di-substituted SF₆ compounds. The basis set used in this work is of double-ζ plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. These methods have been carefully calibrated [J.C. Rienstra-Kiracofe, G.S. Tschumper, H.F. Schaefer, S. Nandi, G.B. Ellison, Chem. Rev. 102 (2002) 231]. The equilibrium configurations of the anions and are found to be a zigzag geometry with ²A electronic state. Three different types of the neutral-anion energy separation reported in this work are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). The most reliable adiabatic electron affinities of the mono-, di-substituted SF₆ compounds obtained at the KMLYP function are 1.48 eV (SF₆), 3.20 eV (SF₅Cl), 3.49 eV (SF₅Br), 1.59 eV (SF₅CF₃), 3.21 eV (CF₃SF₄Cl), 3.59 eV (CF₃SF₄Br), 1.36 eV (CF₃SF₄CH₃), 2.32 eV (CF₃SF₄CF₃), respectively.     

Protonation of group 14 oxides: the proton affinity of SnO

Molecular orbital calculations are reported for the monoxides, XO, of group 14 elements (X = C, Si, Ge and Sn) and for both isomers, XOH⁺ and HXO⁺, of the protonated monoxides. Structure optimisation has been carried out using the Density Functional Theory employing the B3LYP procedure and at both Hartree-Fock and MP2 (full) levels, all with a variety of medium-sized Gaussian basis sets. In all XO molecules the oxygen atom is the preferred site for protonation, except when X = C where HCO⁺ is the lower energy isomer. Barriers to interconversion between the two isomers XOH⁺ and HXO⁺ are over-estimated by the Hartree-Fock calculations, but with wave functions that include electron correlations they generally fall into the range 27-44 kcal mol⁻¹. Proton affinities increase as the atomic number of X increases, and values calculated by averaging over all wave functions that include electron correlation, give the following proton affinities: for CO, 141.5; for SiO, 189.3; for GeO, 196.1; and for SnO, 215.6 (all in kcal mol⁻¹).     

Understanding the acid-base properties of adenosine: the intrinsic basicities of N1, N3 and N7

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.     

Density functional theory rationalization of the substituent effects in trifluoromethyl-pyridinol derivatives

The influence of α-substitution in the structure, bonding and thermochemical properties of trifluoromethyl-pyridinol derivatives and their protonated counterparts has been studied by means of density functional theory. The geometries of the neutral and protonated species were optimized at the B3-LYP/6-311G(d,p) level of theory. Final energies were obtained through single point B3-LYP/6-311+G(3df,2p) calculations.The relative orientation of the different substituents within the heterocycle ring favours the formation of unexpected intramolecular hydrogen bonds (IHB), which have been characterized by means of the Atoms in Molecules theory of Bader. Although weak, these IHB are of great importance for understanding the gas phase structure and the thermodynamical properties of these compounds. Surprisingly, most of the substituted investigated pyridinols present proton affinities below or close to that calculated for the unsubstituted pyridine molecule. Only pyridinols bearing strong σ or π donor activating groups show proton affinities greater than that of pyridine.     

Coupling characteristics and proton transfer mechanisms of guanine–Na monohydrate

The coupling characteristics and the proton transfer mechanisms of guanine–Na⁺ monohydrate are determined in this investigation after the implementation of the geometry optimization and the harmonic vibrational frequency calculations. There are two elementary coupling modes: the interaction of monohydrated sodium ion with two heteroatoms which form a ringed coupling, and hydrogen-bond involved coupling mode. Two potential reaction pathways, coupling mode and hydration have been taken into account, and the accurate values of binding energy are corrected for basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE). Relative energies of the hydrated guanine–sodium ion complexes indicate that the ringed-coupling complexes are predominant geometries with much lower energies. Monohydrated sodium ion coupling with O6 and N7 generates the most stable geometry with a five-member cycle. Sodium ion plays an important role in the tautomerization for guanine–sodium ion complexes. This investigation indicates that the stable cation-π complexes cannot be optimized for guanine–sodium ion monohydrate. Amino-involved coupling often gives rise to a twisted four-membered cycle with unrealistic distribution of positive charge and higher energies. The rotation of amino group is likely to lead to the redistribution of the base pair hydration bonding. Effective distribution of the positive charge is an important factor in the stabilization of biological systems and binding energies for the monohydrated guanine–sodium ion complexes. The enolic coupling complex has the higher energy than the keto type due to the hindrance for the positive charge.     

The measurement of high proton affinities for a variety of metallic compounds: a new approach by flame-ion mass spectrometry

A small amount (≤ 10⁻⁶ mol fraction) of four alkaline earth metals, tin and yttrium were introduced into five, premixed, fuel-rich, H₂–O₂–N₂ flames at atmospheric pressure in the temperature range 1820–2400 K. Aqueous salt solutions of the metals were sprayed into the premixed flame gas as an aerosol using an atomizer technique. Ions in a flame were observed by sampling flame gas through a nozzle into a mass spectrometer. The concentrations of the major neutral metallic species present in the flame were calculated from thermodynamic data currently available. The principal metallic ions observed were AOH⁺ (A = Mg, Ca, Sr, Ba, Sn) and A(OH)₂⁺ (A = Y), formed initially by proton transfer to AO and OAOH from H₃O⁺, a natural flame ion. Except for Mg, the ions were also produced by chemi-ionization processes. By adjusting the concentration(s) of the salt solution in the atomizer, it was found that a pair of ions could be brought into equilibrium within the time scale of the flame; the pairs included H₃O⁺ with a metal ion or two metallic ions. Because water is a major product of combustion, a very large difference in proton affinity PA⁰(AO) − PA⁰(H₂O) ≤ 490 kJ mol⁻¹ (117 kcal mol⁻¹) could be attempted for the proton transfer equilibrium. Using PA⁰(H₂O) = 691.0 kJ mol⁻¹ (165.2 kcal mol⁻¹) as a reference base to anchor the proton affinity scale, ion ratio measurements led to proton affinity PA⁰ values of 766, 912, 1004, 1184, 1201, and 1222 kJ mol⁻¹ (183, 218, 240, 283, 287, and 292 kcal mol⁻¹) corrected to 298 K for OYOH, SnO, MgO, CaO, SrO, and BaO, respectively; of these, only the value for OYOH has not been reported previously. If it is assumed that the neutral thermodynamic data are correct (although some appear to be in error), the uncertainties in the PA results reported here are ± 21 kJ mol⁻¹ (5 kcal mol⁻¹). The realization that these equilibria can be achieved in flames provides a new approach to consolidate and build the high end of the proton affinity ladder, primarily of metallic species which are not accessible at lower temperatures.     

Marked variations of proton release energy of the G–M (M = Li, Na) in the water circumstance

The variations of N1–H proton release energy of G–M (M = Li, Na) cation have been investigated employing density functional theory using B3LYP/6-31++G^**//B3LYP/6-31+G^* method. There are three modes (NO mode, N mode and O mode) when the hydrated-M⁺ bonds to guanine. The bonding energy of the hydrated M⁺ to the guanine reduces following the increase in the number of water molecules. The proton release energies of the G–M⁺ complexes are calculated at the condition of the different numbers of water molecules and the different modes of water molecules bonded on the G–M⁺. The results show that the difference of proton release energy on three modes is very small, and the proton release energies of the Na⁺ complexes are slightly larger than those of the Li⁺ complexes. The effect on the N1–H proton release is very small when the water molecules bond on the M⁺ cation, but the effect is very large when the water molecule bonds on the N1–H proton and the proton releases as the hydrated proton. The IR vibrational frequencies of the hydrated G–M⁺ complexes are calculated using analytic second derivative methods at the B3LYP/6-31+G^* level. The vibrational frequency analyses show that the changes of the vibrational frequency are consistent with the changes of geometry and the changes of the N1–H proton release energy. The N1–H proton release (N1–H proton release energy: 45–60 kcal/mol) of the guanine occurs easily under the biological environment.