Correlating acidities, electron affinities, and bond dissociation energies. Measure one, get all three!

Bond energies, acidities, and electron affinities are related in a thermodynamic cycle, and by measuring two of these quantities one can derive the third. This procedure is most often used to determine bond dissociation energies. In this work, we show that Delta H(o)(acid)(HX), EA(X(*)), and BDE(HX) are all linearly related for specific classes of compounds (e.g., alcohols and carboxylic acids), and therefore, only one of these quantities is needed to determine the others. This should simplify thermodynamic determinations and enable hundreds of new values to be obtained from already existing data in the literature. The intercepts obtained from plots of Delta H(o)(acid)(HX) vs EA(X(*)) provide bond energies which correspond to BDE(HX) when EA(X(*)) = 0. The results for eight different types of compounds are provided and some of these values are discussed. Sensitivity factors are obtained from the slopes of these plots, and their sign (+ vs -) can be predicted by considering physical effects such as hybridization and resonance.     

Improved proton affinity measurements for proline and modified prolines using triple quadrupole and ion trap mass spectrometers

Proton affinity (PA) of compounds such as proline, cis-3-methylproline, cis-3-ethylproline, cis-3-isopropylproline and cis-3-isopentanylproline was determined by kinetic method with amines as the reference bases. The effective temperatures determined using ion trap and triple quadrupole mass spectrometers were found to be significantly different. In the case of the triple quadrupole instruments, the effective temperature depends significantly on the collision energy. The influence of the apparent basicity (GBapp) on the effective temperature may be used to estimate the difference in protonation entropy (DeltaDeltaS degrees) between the sample and reference compounds. In case of the ion trap mass spectrometer, the variation of the effective temperature as a function of the excitation amplitude is small, so it is difficult to account for the contribution of the entropy effects to the proton affinity value. A better estimation of the PA and DeltaDeltaS degrees values for the investigated molecules is obtained by combining the GBapp and Teff data pairs that are obtained from both the mass spectrometers.     

脂肪醇盐离子质子亲和能与量子化学参数的关系

采用半经验量子化学方法（MNDO，AM1和PM3）、从头算（采用STO-3G，3-21G，6-31G，6-31G^*,^6-31G^**,6-311G,6-311G^*和6-311G^**基组）HF方法计算羟基和6种脂肪醇盐离子以获得电子结构数据。通过相关分析发现脂肪醇盐离子中的氧原子净电荷，HOMO能级与质子亲和能之间具有良好的线性的相关性。     

Calculation of the proton affinities of polychlorobenzenes and the activation energies of 1,2-hydrogen shifts in arenonium ions

The proton affinities of benzene, chlorobenzene and polychlorobenzenes with the common formula C₆Cl _n H_6–n (n=0–6) have been calculated by the AM1 method. The proton affinity averaged over the protonated isomers increases monotonically asn growing from 0 to 5, and then decreases when passing from pentato hexachlorobenzene. The energies of proton addition to the different positions in the polychlorobenzene molecules have been estimated. It has been found that unsubstituted carbon atoms are preferred for proton attack. The positions with the highest proton affinity are the carbon atoms with the largest negative charges. The activation energies of 1,2-hydrogen shifts in arenonium ions of the polychlorobenzenes have been calculated.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1213–1217, July, 1993.     

A theoretical study of five nitrates: Electronic structure and bond dissociation energies

Three density-functional methods (B3P86, B3PW91, and B3LYP) are employed to investigate the O–NO₂ bond lengths, frontier orbital energies, and O–NO₂ bond dissociation energies (BDEs) of n-propyl nitrate (NPN), isopropyl nitrate (IPN), 2-ethylhexyl nitrate (EHN), triethylene glycol dinitrate (Tri-EGDN), and tetraethylene glycol dinitrate (Tetra-EGDN). It is found that the O–NO₂ bond lengthens (destabilizes) in the order of IPN, NPN, EHN, Tetra-EGDN, and Tri-EGDN. From the data of frontier orbital energies (E_HOMO, E_LUMO), and energy gaps (ΔE), we estimate the relative thermal stability ordering of five nitrates and their corresponding radicals. The predicted BDEs of O–NO₂ bond in NPN, IPN, EHN, Tri-EGDN, and Tetra-EGDN, are 176.6, 174.5, 168.1, 156.1, and 159.3 kJ mol⁻¹, respectively. Based on the finding that the present results of BDEs are well coincident with the experimental results of apparent activation energies from the literature, we can draw a conclusion that the experimental thermolysis of five nitrates is only unimolecular homolytical cleavage of the O–NO₂ bonds.     

Protonation of glycine and alanine: proton affinities, intrinsic basicities and proton transfer path

Proton affinities and intrinsic basicities for nitrogen and oxygen protonation in the gas phase of the amino acids glycine and alanine were calculated using density functional theory (DFT) and ab initio methods at different levels of theory from Hartree-Fock (HF) to G2 approximations. All methods gave good agreement for proton affinities for nitrogen protonation for both amino acids. However, dramatic differences were found between DFT, MP4//MP2, and G2 results on one hand, and MP4//HF results on the other to the calculation of structural and energetic characteristics of oxygen protonation in glycine and alanine. An investigation into the source of these differences revealed that electron correlation effects are chiefly responsible for the differences in calculated oxygen proton affinities between the various methods. It has been found that proton transfer between nitrogen and oxygen protonation sites in both amino acids occurs without a transfer path barrier when correlated methods were used to calculate the path energetics.     

Quantum mechanical studies of the protonation and NBr bond dissociation of the biologically important N-bromosuccinimide

N-Bromosuccinimide (NBS) is a brominating and oxidizing agent that is used as a source of bromine. The proton affinities, the tautomeric forms and NBr bond dissociation of NBS have been computed using the B3LYP functional as implemented in the density functional approach. The electronic structures of all possible tautomeric forms of NBS have been thoroughly investigated. The keto form of NBS has been shown to be more stable than any other tautomeric forms. The geometries and relative energies for various stationary structures were determined. The results indicate clearly that O-site protonation is strongly favored over N-site protonation for the studied compound in case of mono- and di-protonation. The bond dissociation energies (BDEs), involving the formation of the bromine radical, cation, and anion, of the NBr bond have been investigated. The NBr BDE of the Br radical formation is lower than that of the Br anion or cation. These conclusions are in good agreement with the experimental results.     

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.     

Spectroscopic calculations of CH and OH bond dissociation energies for aldehydes, ketones, acids, and alcohols

CH and OH bond dissociation energies were calculated by the spectroscopic and quantum-chemical methods for aldehydes, ketones, acids, and alcohols. The spectroscopic values of CH and OH bond dissociation energies were obtained from the fundamental absorption bands by the variational method in an anharmonic approximation using the Morse-anharmonic basis set. Quantum-chemical calculations were carried out using the 6-311G(3df,3pd)/B3LYP basis set. It is discussed how the bond dissociation energies change with the structure of the molecule.     

Theoretical analysis on the hydrogen bonding and reactivity that associated with the proton transfer reaction of carboxylic acid dimers and their monosulfur derivatives

Carboxylic acid dimers and their monosulfur derivatives are investigated by density functional theory calculations. Basis set superposition error (BSSE) counterpoise correction is included to compare the influence of BSSE on the interaction energies as well as on the geometries. The nature of hydrogen bond is determined on the basis of atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Good correlations have been established between H‐bond length versus AIM topological parameter, orbital interaction, and barrier height for proton transfer. The reactivity behavior along the reaction path of the double proton transfer reaction has also been studied. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

CH3I同步辐射光电离及生成焓、键能和质子亲合势的测定

在超声射流冷却条件下用VUV同步辐射研究了CH3I分子的光电离过程。测定了CH3I光电离及解离电离产生的CH3I^+, CH3^+和I^+的出现势, 结合已确认的热力学数据, 估算出体系中有关离子的标准生成焓、分子和分子离子的键能、自由基的质子亲合势及母体离子的解离能等数据。对CH3I分子VUV光解离电离通道进行了分析。     

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.     

Different Protonation Equilibria of 4‐Methylimidazole and Acetic Acid

Dynamic protonation equilibria in water of one 4‐methylimidazole molecule as well as for pairs and groups consisting of 4‐methylimidazole, acetic acid and bridging water molecules are studied using Q‐HOP molecular dynamics simulation. We find a qualitatively different protonation behavior of 4‐methylimidazole compared to that of acetic acid. On one hand, deprotonated, neutral 4‐methylimidazole cannot as easily attract a freely diffusing extra proton from solution. Once the proton is bound, however, it remains tightly bound on a time scale of tens of nanoseconds. In a linear chain composed of acetic acid, a separating water molecule and 4‐methylimidazole, an excess proton is equally shared between 4‐methylimidazole and water. When a water molecule is linearly placed between two acetic acid molecules, the excess proton is always found on the central water. On the other hand, an excess proton in a 4‐methylimidazole‐water‐4‐methylimidazole chain is always localized on one of the two 4‐methylimidazoles. These findings are of interest to the discussion of proton transfer along chains of amino acids and water molecules in biomolecules.     

Sugar amino acids and related molecules: Some recent developments

To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started working on many new concepts that can help to assimilate knowledge-based structural diversities more efficiently than ever before. Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. In recent years, sugar amino acids have been used extensively in the area of peptidomimetic studies. Advances made in the area of combinatorial chemistry can provide the necessary technological support for rapid compilations of sugar amino acidbased libraries exploiting the diversities of their carbohydrate frameworks and well-developed solid-phase peptide synthesis methods. This perspective article chronicles some of the recent applications of various sugar amino acids, furan amino acids, pyrrole amino acids etc. and many other related building blocks in wide-ranging peptidomimetic studies     

Calculation of the proton affinities of polyfluorobenzenes and the activation energies for 1,2-hydrogen shifts in their carbocations

Isolated polyfluorobenzene (PFB) molecules and their protonated forms are investigated by the AM1 method with full geometry optimization. The proton affinities of PFB are estimated for different protonated positions. The proton affinity of PFB averaged over all isomers is shown to decrease monotonically as the number of fluorine atoms in the molecule increases. The relative populations of different isomers of arenonium ions (AI) formed by PFB protonation are determined. From the calculated data, the value of ⁺ for the F atom in theipso-position is estimated as 1.00. The activation energies of the 1,2-hydrogen shifts in AI are calculated. The dependences of the proton affinity and the activation energies of 1,2-hydrogen shifts on the number of halogen atoms are found to have distinct characters for PFB and polychlorobenzenes. The physical reasons for these difference are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1878–1882, November, 1993.     

Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components

Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3, 5-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set. PLS is applied to correlate the CoMFA data with either calculated AM1 proton affinities or with experimental pKa values. The possibility of making a prediction of pKa values directly from 3D structures of the monomers for polynucleotides is also shown. The influence of the superposition criteria and of conformational changes along the glycosidic bond on the pKa prediction are studied as well.     

Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes

The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Excitation energies, electron affinities and ionization potentials of the transition metals V, Cr and Mn

 Configuration interaction calculations were carried out for neutral ground and excited states and positively and negatively ionized states of the V, Cr and Mn atoms. Energy convergence with respect to systematic expansion of both the one-electron and configuration bases was investigated for valence correlation. Contributions from core electrons to the differential correlation energies and relativistic effects were evaluated separately. Assuming additivity of these contributions, excitation energies, electron affinities and ionization potentials of the atoms were obtained. All calculated values were in excellent agreement with the observed values within a deviation of 0.056 eV except for the electron affinity of the V atom, which had a calculated value 0.110 eV larger than the experimental value. Received: 9 August 2000 / Accepted: 26 October 2000 / Published online: 3 April 2001