Proton Affinity Calculations with High Level Methods

Molecular Tuning of Reactivity of Zeolite Protons in HZSM-5

In acidic HZSM-5 zeolite, the reactivity of a methanol molecule interacting with the zeolite proton is amenable to modification via coadsorbing a stochiometric amount of an electron density donor E to form the [(E)(CH3OH)(HZ)] complex. The rate of the methanol in this complex undergoing dehydration to dimethyl ether was determined for a series of E with proton affinity (PA) ranging from 659 kJ mol-1 for C6F6 to 825 kJ mol-1 for C4H8O and was found to follow the expression: Ln(Rate) - Ln(RateN2) = β(PA - PAN2)γ, where E = N2 is the reference and β and γ are constants. This trend is probably due to the increased stability of the solvated proton in the [(E)(CH3OH)(HZ)] complex with increasing PA. Importantly, this is also observed in steady-state flow reactions when stoichiometric quantities of E are preadsorbed on the zeolite. As demonstrated with E being D2O, the effect on methanol reactivity diminishes when E is present in excess of the [(E)(CH3OH)(HZ)] complex. It is proposed that the methanol dehydration reaction involves [(E)(CH3OH)(CH3OH)(HZ)] as the transition state, which is supported by the isotopologue distribution of the initial dimethyl ether formed when a flow of CH3OH was passed over ZSM-5 containing one CD3OH per zeolite proton. The implication of this on the mechanism of catalytic methanol dehydration on HZSM-5 is discussed.

Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media

The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.

Green Approach for the Synthesis of Chalcogenyl- 2,3-dihydrobenzofuran Derivatives Through Allyl-phenols/ Naphthols and Their Potential as MAO-B Inhibitors

This work presents the design, synthesis, and MAO-B inhibitor activity of a series of chalcogenyl-2,3-dihydrobenzofurans derivatives. Using solvent- and metal-free methodology, a series of chalcogen-containing dihydrobenzofurans 7-9 was obtained with yields ranging from 40% to 99%, using an I2 /DMSO catalytic system. All compounds were fully structurally characterized using 1 H and 13 C NMR analysis, and the unprecedented compounds were additionally analyzed using high-resolution mass spectrometry (HRMS). In addition, the mechanistic proposal that iodide is the most likely species to act in the transfer of protons along the reaction path was studied through theoretical calculations. Finally, the compounds 7b-e, 8a-e, and 9a showed great promise as inhibitors against MAO-B activity.

Aliphatic tertiary amine catalysed urethane formation - a combined experimental and theoretical study

A kinetic and mechanistic investigation of the alcoholysis of phenyl isocyanate (PhNCO) using stoichiometric butan-1-ol (BuOH) in acetonitrile in the presence of different tertiary amine catalysts was performed. The reaction mechanisms in the absence and presence of experimentally applied catalysts were described by using the G3MP2BHandHLYP composite method. The apparent activation energies obtained from the calculations were in good agreement with the experimental data (ΔΔE = <2 kJ mol^-1). Both experimental and theoretical results proved the important effect of tertiary amine catalysts on urethane formation. These results can aid in polyurethane catalyst design and development.

Experimental and Theoretical Study of Cyclic Amine Catalysed Urethane Formation

The alcoholysis of phenyl isocyanate (PhNCO) using stoichiometric butan-1-ol (BuOH) in acetonitrile in the presence of different cyclic amine catalysts was examined using a combined kinetic and mechanistic approach. The molecular mechanism of urethane formation without and in the presence of cyclic amine catalysts was studied using the G3MP2BHandHLYP composite method in combination with the SMD implicit solvent model. It was found that the energetics of the model reaction significantly decreased in the presence of catalysts. The computed and measured thermodynamic properties were in good agreement with each other. The results prove that amine catalysts are important in urethane synthesis. Based on the previous and current results, the design of new catalysts will be possible in the near future.

Proton affinity and gas phase basicity of diamandoid molecules: diamantane to C131H116

Calculated proton affinities (PAs) and gas phase basicities (GPBs) are reported for diamantane (C₁₄H₂₀), triamantane (C₁₈H₂₄), 'globular and planar' isomers of tetramantane (C₂₂H₂₈) and pentamantane (C₂₆H₃₂), and for one 'globular' isomer of each of the larger diamondoid molecules: C₅₁H₅₈, C₇₈H₇₂, C₁₀₂H₉₀, and C₁₃₁H₁₁₆. Assuming C_xH_y as the parent diamondoid molecule, we calculated PA and GPB values for a variety of C_xH_y+1⁺ isomers, as well as for the reaction C_xH_y + H⁺ yielding C_xH_y-1⁺ + H₂(g); the latter is slightly favored based on GPB values for diamantane through pentamantane, but less favored compared to certain C_xH_y+1⁺ isomers of C₅₁H₅₈, C₁₀₂H₉₀, and C₁₃₁H₁₁₆. Indeed, the GPB values of C₅₁H₅₈, C₁₀₂H₉₀, and C₁₃₁H₁₁₆ classifiy them as 'superbases'. Calculations that had the initial location of the proton in an interstitial site inside the diamondoid molecule always showed the H having moved to the outside of the diamondoid molecule; for this reason, we focused on testing a variety of initial configurations with the proton placed in an initial position on the surface. Additional protons were added to determine the limiting number that could be, per these calculations, taken up by the diamondoid molecules and the maximum number of protons are shown in parentheses: C₁₄H₂₀(2), C₁₈H₂₄(3), C₂₂H₂₈(3), C₂₆H₃₂(3), C₅₁H₅₈(4). Bader charge distributions obtained for C_xH_y+1⁺ isomers (for diamantane through pentamantane) suggest that the positive charge is essentially completely delocalized over all the H atoms. NMR spectra were calculated for different isomers of C₁₄H₁₉⁺, and compared to the published NMR spectrum for when diamantane was mixed with magic acid and H₂(g) was produced.

Computational Study of Catalytic Urethane Formation

Polyurethanes (PUs) are widely used in different applications, and thus various synthetic procedures including one or more catalysts are applied to prepare them. For PU foams, the most important catalysts are nitrogen-containing compounds. Therefore, in this work, the catalytic effect of eight different nitrogen-containing catalysts on urethane formation will be examined. The reactions of phenyl isocyanate (PhNCO) and methanol without and in the presence of catalysts have been studied and discussed using the G3MP2BHandHLYP composite method. The solvent effects have also been considered by applying the SMD implicit solvent model. A general urethane formation mechanism has been proposed without and in the presence of the studied catalysts. The proton affinities (PA) were also examined. The barrier height of the reaction significantly decreased (∆E₀ > 100 kJ/mol) in the presence of the studied catalysts, which proves the important effect they have on urethane formation. The achieved results can be applied in catalyst design and development in the near future.

Influence of Reduced Field Strength on Product Ion Formation in High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS)

Classical ion mobility spectrometers (IMS) operated at ambient pressure, often use atmospheric pressure chemical ionization (APCI) sources to ionize organic compounds. In APCI, reactant ions ionize neutral analyte molecules via gas-phase ion-molecule reactions. The positively charged reactant ions in purified, dry air are H₃O⁺, NO⁺, and O₂^+•. However, the hydration of reactant ions in classical IMS operated at ambient pressure renders ionization of certain analytes difficult. In contrast to classical IMS operated at ambient pressure, High Kinetic Energy Ion Mobility Spectrometers (HiKE-IMS) are operated at a decreased pressure of 10-40 mbar, allowing operation at high reduced electric field strengths of up to 120 Td. At such high reduced field strengths, ions reach high effective temperatures causing collision-induced cluster dissociation of the hydrated gas-phase ions, allowing ionization of nonpolar and low proton affinity analytes. The reactant ion population, consisting of H₃O⁺(H₂O)_n, NO⁺(H₂O)_m, and O₂^+•(H₂O)_p with an individual abundance that strongly depends on the reduced field strength, differs from the reactant ion population in IMS operated at ambient pressure, which affects the ionization of analyte molecules. In this work, we investigate the influence of reduced field strength on the product ion formation of aromatic hydrocarbons used as model substances. A HiKE-IMS-MS coupling was used to identify the detected ion species. The results show that the analytes form parent cations via charge transfer with NO⁺(H₂O)_m and O₂^+•(H₂O)_p depending on ionization energy and protonated parent molecules via proton transfer and ligand switching with H₃O⁺(H₂O)_n mainly depending on proton affinity.

Benchmark calculations of proton affinity and gas-phase basicity using multilevel (G4 and G3B3), B3LYP and MP2 computational methods of para-substituted benzaldehyde compounds

This study presents the benchmark calculations of proton affinities (PAs) and gas-phase basicities (GBs) of 8-para substituted benzaldehyde compounds using the multilevel model chemistries (G3B3 and G4), density-functional quantum model (B3LYP) and ab initio model (MP2). The results show that the computed properties are strongly correlated with the available experimental data. The PAs and the GBs of other eight para-substituted benzaldehyde compounds, for which the experimental data does not currently exist, have been calculated using G3B3 and B3LYP methods. The correlations between the experimental PAs and GBs with the computed properties such as PA, GB, chemical properties (bond lengths, electron density and δ¹ H NMR chemical shift) of the investigated benzaldehydes have been studied and statistically analyzed. The influence of the substituted groups has been discussed in terms of inductive effect and electron donating and electron withdrawing effect. The results obtained show that the chemical properties of the benzaldehyde compounds are controlled by the strong coupling between the CHO group and the nature of the para-substituent groups through the benzene ring as a conducting linkage.

Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices

RATIONALE

For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS analysis, matrix selection is critical and a new matrix could enable more efficient and rapid structural analysis.

METHODS

We hypothesized that nucleobase derivatives could act as matrices more efficiently than the currently used matrices for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrices, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide analysis.

RESULTS

Six of the 16 nucleobase derivatives acted as matrices for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed.

CONCLUSIONS

Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrices in oligonucleotide sequencing.

Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors

Covalent inhibition has undergone a resurgence and is an important modern-day drug design and chemical biology approach. To avoid off-target interactions and to fine-tune reactivity, the ability to accurately predict reactivity is vitally important for the design and development of safer and more effective covalent drugs. Several ligand-only metrics have been proposed that promise quick and simple ways of determining covalent reactivity. In particular, we examine proton affinity and reaction energies calculated with the density functional B3LYP-D3/6-311+G**//B3LYP-D3/6-31G* method to assess the reactivity of a series of α,β-unsaturated carbonyl compounds that form covalent adducts with cysteine. We demonstrate that while these metrics correlate well with experiment for a diverse range of small reactive molecules these approaches fail for predicting the reactivity of drug-like compounds. We conclude that ligand-only metrics such as proton affinity and reaction energies do not capture determinants of reactivity in situ and fail to account for important factors such as conformation, solvation, and intermolecular interactions.

Alkali Metal Cation Affinities of Neutral Maingroup-Element Hydrides across the Periodic Table

We have carried out an extensive quantum chemical exploration of gas-phase alkali metal cation affinities (AMCAs) of archetypal neutral bases across the periodic system using relativistic density functional theory. One objective of this work is to provide an intrinsically consistent set of values of the 298 K AMCAs of all neutral maingroup-element hydrides XH_n of groups 15–18 along the periods 1–6. Our main purpose is to understand these trends in terms of the underlying bonding mechanism using Kohn–Sham molecular orbital theory together with a canonical energy decomposition analysis (EDA). We compare the trends in XH_n AMCAs with the trends in XH_n proton affinities (PAs). We also examine the differences between the trends in AMCAs of the neutral XH_n bases with those in the corresponding anionic XH_n–1^– bases. Furthermore, we analyze how the cation affinity of our neutral Lewis bases changes along the group-1 cations H⁺, Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺.

On the Use of Popular Basis Sets: Impact of the Intramolecular Basis Set Superposition Error

The magnitude of intramolecular basis set superposition error (BSSE) is revealed via computing systematic trends in molecular properties. This type of error is largely neglected in the study of the chemical properties of small molecules and it has historically been analyzed just in the study of large molecules and processes dominated by non-covalent interactions (typically dimerization or molecular complexation and recognition events). In this work we try to provide proof of the broader prevalence of this error, which permeates all types of electronic structure calculations, particularly when employing insufficiently large basis sets.

Alternated Branching Ratios by Anomaly in Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pairs of 1-Methylcytosine with 1-Methylguanine and 9-Methylguanine

A comparative study on the proton-bound complexes of 1-methylcytosine (1-mC) with 1-methylguanine (1-mG) and 9-methylguanine (9-mG), [1-mC:1-mG:H]⁺ and [1-mC:9-mG:H]⁺, respectively, was carried out using energy-resolved collision-induced dissociation (ER-CID) experiments in combination with quantum chemical calculations. In ER-CID experiments, the measured survival yields indicated an essentially identical stability for the two proton-bound complexes. In comparison with the lowest-energy structures and base-pairing energetics predicted at the B3LYP/6-311+G(2d,2p) theory level, both complexes produced in this study were suggested to be proton-bound Hoogsteen base pairs. Curiously, despite the similarity in structures, binding energetics, and potential energy surfaces predicted by the B3LYP theory, the fragment branching ratios exhibited an intriguing alternation between the two proton-bound Hoogsteen base pairs. The CID of [1-mC:1-mG:H]⁺ produced protonated cytosines, [1-mC:H]⁺, more abundantly than [1-mG:H]⁺, whereas that of [1-mC:9-mG:H]⁺ gave rise to a more pronounced production of protonated guanines, [9-mG:H]⁺. However, using the proton affinities of moieties predicted by the high-accuracy methods, including CBS-QB3 and the Guassian-4 theory, the anomaly known for [Cytosine:Guanine:H]⁺ (J. Am. Soc. Mass Spectrom. 29, 2368-2379 (2018)) successfully accounted for the alternated branching ratios. Thereby, the anomaly, more specifically, the production of proton-transferred fragments of O-protonated cytosines in the CID of proton-bound Hoogsteen base pairs, is indeed real, which is disclosed as the alternated branching ratios in the CID spectra of [1-mC:1-mG:H]⁺ and [1-mC:9-mG:H]⁺ in this study. Graphical Abstract .

Prediction of proton affinities of organic molecules using the any-particle molecular-orbital second-order proton propagator approach

We assess the performance of the recently developed any-particle molecular-orbital second-order proton propagator (APMO/PP2) scheme [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes and R. Flores-Moreno, J. Chem. Phys., 2013, 138, 194108] on the calculation of gas phase proton affinities (PAs) of a set of 150 organic molecules comprising several functional groups: amines, alcohols, aldehydes, amides, ketones, esters, ethers, carboxylic acids and carboxylate anions. APMO/PP2 PAs display an overall mean absolute error of 0.68 kcal mol^-1 with respect to experimental data. These results suggest that the APMO/PP2 method is an alternative approach for the quantitative prediction of gas phase proton affinities. One novel feature of the method is that a PA can be obtained from a single calculation of the optimized protonated molecule.

The Utility of Calculated Proton Affinities in Drug Design: A DFT Study

Computer-aided drug design comprises several predictive tools, which can calculate various properties of the candidates under development. Proton affinity (PA) is related to pKa (the negative log of the acid dissociation constant (Ka)) one of the fundamental physical properties of drug candidates, determining their water solubility and thus their pharmacokinetic profile. The following questions therefore emerged: to what extent are PA predictions useful in drug design, and can they be reliably used to derive pKa values? Using density functional theory (DFT), it was established that for violuric acid, with three ionisation groups, the PAs correlate well with the measured pKas (R2 = 0.990). Furthermore, an excellent correlation within the amiloride compound family was achieved (R2 = 0.922). In order to obtain correlations for larger compound collections (n = 210), division into chemical families was necessary: carboxylic acids (R2 = 0.665), phenols (R2 = 0.871), and nitrogen-containing molecules (R2 = 0.742). These linear relationships were used to predict pKa values of 90 drug molecules with known pKas. A total of 48 % of the calculated values were within 1 logarithmic unit of the experimental number, but mainstream empirically based methods easily outperform this approach. The conclusion can therefore be reached that PA values cannot be reliably used for predicting pKa values globally but are useful within chemical families and in the event where a specific tautomer of a drug needs to be identified.

Fast and accurate prediction of proton affinities: revisiting the extended Koopmans' theorem for protons

In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs). The performance of these schemes has been tested on a set of 300 organic molecules containing diverse functional groups. The APMO/KT scheme scaled by functional group (APMO/KT-SC-FG) displays an overall mean absolute error of 1.1 kcal mol^-1 with respect to experimental data. Its performance in PA calculations is similar to that of post-Hartree-Fock composite methods or that of the APMO second order proton propagator (APMO/PP2) approach. The APMO/KT-SC-FG scheme is also employed to predict PAs of polyfunctional molecules such as the Nerve Agent VX and the 20 common α-amino acids, finding excellent agreement with available theoretical and/or experimental data. The accuracy of the predictions demonstrates that the APMO/KT-SC-FG scheme is a low-cost alternative to adiabatic methods for the calculation of accurate PAs. One of the most appealing features of the APMO/KT-SC-FG scheme, is that PAs can be derived from one single-point APMO Hartree-Fock calculation.

Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase

Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)_n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.

Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism

We have analyzed the structure and bonding of gas‐phase Cl−X and [HCl−X]⁺ complexes for X⁺= H⁺, CH₃⁺, Li⁺, and Na⁺, using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl⁻ and HCl for the various cations. The Cl−X bond becomes longer and weaker along X⁺ = H⁺, CH₃⁺, Li⁺, and Na⁺. Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn–Sham molecular orbital (KS‐MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities.

(15)N NMR Spectroscopy, X-ray and Neutron Diffraction, Quantum-Chemical Calculations, and UV/vis-Spectrophotometric Titrations as Complementary Techniques for the Analysis of Pyridine-Supported Bicyclic Guanidine Superbases

Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution.