Proton affinity of peroxyacetyl nitrate. A computational study of topical proton affinities

The structure and energetics of the peroxyacetyl nitrate conformers syn- and anti-PAN and several cations formed by PAN protonation were investigated by a combination of density functional theory and ab initio calculations. syn-PAN is the more stable conformer that is predicted to predominate in gas-phase equilibria. The acetyl carbonyl oxygen was found to be the most basic site in PAN, the oxygen atoms of the peroxide and NO(2) groups being less basic. The 298 K proton affinity of syn-PAN was calculated as 759-763 kJ mol(-1) by effective QCISD(T)/6-311 + G(3df,2p) and 771-773 kJ mol(-1) by B3-MP2/6-311 + G(3df,2p). The calculated values are 25-39 kJ mol(-1) lower than the previous estimate by Srinivasan et al. (Rapid Commun. Mass Spectrom. 1998; 12: 328) that was based on competitive dissociations of proton-bound dimers (the kinetic method). The calculated threshold dissociation energies predicted the formation of CH(3)CO(+) + syn - HOONO(2) and CH(3)COOOH + NO(2)(+) to be the most favorable fragmentations of protonated PAN that required 83 and 89 kJ mol(-1) at the respective thermochemical thresholds at 298 K. The previously observed dissociation to CH(3)COOH + NO(3)(+) was calculated by effective QCISD(T)/6-311 + G(3df,2p) to require 320 kJ mol(-1). The disagreement between the experimental data and calculated energetics is discussed.     

A computational study of gas-phase acidity and basicity of azulene-based uracil analogue

Structural Chemistry - In this paper, we suggest a computational scheme for the theoretical estimation of gas-phase acidity and basicity of azulene-based uracil analogue. The proton affinities...     

Proton affinity of five‐membered heterocyclic amines: Assessment of computational procedures

Ab initio quantum chemical calculations, G3B3, second‐order Møller–Plesset (MP2), and the hybrid density functional method B3LYP were employed to compute the proton affinities of 24 heterocyclic amines. A range of basis sets are employed, starting from double‐ζ polarization quality to triple‐ζ quality basis set with augmented diffuse and polarization function. Experimental values were used to calibrate the performance of various theoretical models. The regioselectivity for the protonation has been unambiguously established by performing B3LYP/6‐31G* calculations on the possible putative sites of attack. For the given series of compounds the performance of B3LYP/6‐31++G** and G3B3 levels of theory have been in excellent agreement with the experimental results with the deviations are of the order comparable with the experimental error. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

The protonation of allene and some heteroallenes, a computational study

Protonation of allene and seven heteroallenes, X = Y = Z, at the terminal and central positions has been studied computationally at the MP2/6-311+G**, B3LYP/6-31+G**, and G3 levels. In all but one case protonation at a terminal position is preferred thermodynamically. The exception is allene, where protonation at C2 giving allyl cation prevails by about 10 kcal/mol over end-protonation, which gives the 2-propenyl cation. In the heteroallenes, protonation at a terminal carbon is strongly favored, activated by electron donation from the other terminal atom. Transition states for identity proton-transfer reactions were found for 10 of the "end-to-end" proton transfers. When the transfer termini are heteroatoms these processes are barrier free. We found no first-order saddle point structures for "center-to-center" proton transfers. An estimate of DeltaH++ for an identity center-to-center proton transfer could be made only for the reaction between the allyl cation and allene; it is approximately 22 kcal/mol higher than DeltaH++ for the end-to-end proton transfer between the 2-propenyl cation and allene. First-order saddle points for the proton transfer from H3S+ to both C1 and C2 of allene were found. The difference in activation enthalpies is 9.9 kcal/mol favoring protonation at C1 in spite of the thermodynamic disadvantage. We infer that protonation of X = Y = Z at central atoms passes through transition states much like primary carbenium (nitrenium, oxenium) cations, poorly conjugated with the attached vinylic or heterovinylic group. Several other processes following upon center protonation were studied and are discussed in the text, special attention being given to comparison of open and cyclic isomers.     

Conformations, protonation sites, and metal complexation of benzohydroxamic Acid. A theoretical and experimental study

A theoretical and experimental study on the structure and deprotonation of benzohydroxamic acid (BHA) has been performed. Calculations at the RHF/cc-pVDZ level, refined by the B3LYP/AUG-cc-pVDZ method, indicate that, in the gas phase, Z amide is the most stable structure of both neutral and deprotonated BHA. (1)H-(1)H nuclear Overhauser enhancement spectroscopy and (1)H-(1)H correlation spectroscopy spectra in acetone, interpreted with ab initio interatomic distances, reveal that BHA is split into the Z and E forms, the [E]/[Z] ratio being 75:25 at -80 degrees C. The formation of E-E, Z-Z, and E-Z dimers has been detected; in the presence of water, the dimers dissociate to the corresponding monomers. The rates of proton exchange within the Z and E forms and between E and Z were measured by dynamic (1)H NMR in the -60 to 40 degrees C temperature range; an increase in water content lowers the rate of exchange of the E isomer. The effect of D(2)O on the NMR signals indicates a fast hydrogen exchange between D(2)O and the E and Z amide forms. The sequence of the acid strength at low temperatures is (N)H(E)) approximately (O)H(E) < (O)H(Z) approximately (N)H(Z). The kinetics of complex formation between BHA and Ni(2+), investigated by the stopped-flow method, show that both neutral BHA and its anion can bind Ni(2+). Whereas the anion reacts at a "normal" speed, the rate of water replacement from Ni(H(2)O)(6)(2+) by neutral BHA is about 1 order of magnitude less than expected. This behavior was interpreted assuming that, in aqueous solution, BHA mainly adopts a closed (hydrogen-bonded) Z configuration, which should open (with an energy penalty) for the metal binding process to occur.     

Proton catalyzed hydrolytic deamination of cytosine: a computational study

Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of ΔG ^≠=140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH ^? catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (E _a = 117  ±  4 kJ/mol).     

Conformational analysis and the binding sites of nitrilotriacetamide: A computational study

The conformational analysis of nitrilotriacetamide has been carried out computationally, at both the semi‐empirical AM1 and density functional theory (DFT) (B3LYP/6‐31+G*) levels of theory. The lowest‐energy conformation predicted with the Monte Carlo search method, using the AM1 model, has two amide functionalities aligned on the same side; however, the DFT calculations at B3LYP/6‐31+G* predicted the global minimum with all three acetamide functionalities on the same side in the gas phase. In the aqueous phase, the DFT results predicted the orientations of amides similar to that of the reported crystal structure. The rotation barriers to transition to different low‐energy conformers of nitrilotriacetamide are lower in energy (5.0 kcal/mol) in water. The molecular electrostatic isopotentials (MESP) generated for the selected conformers at DFT level show that the nitrilotriacetamide could interact more effectively with the sodium chloride surface than that of its monomeric unit nitrilomonoacetamide. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Proton affinity of SO3

Collision-induced dissociation (CID) of the radical cation H₂SO₄⁺ gives the product pairs H₂O⁺+SO₃ and HO+HSO₃⁺ with a 1:3 ratio that is essentially independent of collision energy. Statistical analysis of the two channels indicates that the proton affinity of HO is 3±4 kJ/mol lower than that of SO₃. This can be used to derive PA(SO₃)=591±4 kJ/mol at 0 K and 596±4 kJ/mol at 298 K. Previously, Munson and Smith bracketed the proton affinity as PA(HBr)=584 kJ/mol<PA(SO₃)<PA(CO)=594 kJ/mol. The threshold of 152±16 kJ/mol for formation of H₂O⁺+SO₃ indicates that the barrier to CID is small or nonexistent, in contrast to the substantial barriers to decomposition for H₃SO₄⁺ and H₂SO₄.     

Dehydroaporphines: A protonation study

The representative dehydroaporphines dehydronuciferine (2), dehydrodicentrine (3) and dehydroocopodine (4) initially undergo both N-protonation and C-protonation (at C-7) in CF₃COOH, the C-protonated immonium salts being formed almost completely under equilibration conditions. Applications of these observations to the synthesis of 7-deuteriodehydrodicentrine (7) and 6a,7,7-trideuterionuciferine (8) are described.     

Proton affinity of methyl peroxynitrate

The equilibrium structures, harmonic vibrational frequencies of methyl peroxynitrate, and structures of protonated methyl peroxynitrate have been investigated using ab initio methods. The methods include the single- and double-excitation quadratic configuration (QCISD) methods and the QCISD(T) method, which incorporates a perturbational estimate of the effects of corrected triple excitation. The lowest-energy gas-phase form of protonated methyl peroxynitrate is a complex between CH3OOH and NO2+. The CH3OOH.NO2+ complex is bound by 22 +/- 2 kcal/mol. The estimated proton affinity of methyl peroxynitrate is 178.8 +/- 3 kcal/mol. A general trend for the proton affinity of ROO-NO2 (peroxynitrates) compounds is discussed.     

1,10-Phenanthrolines with tunable luminescence upon protonation: a spectroscopic and computational study

We have synthesized nine 2,9-aryl-substituted 1,10-phenanthrolines (1-9) with the aim of rationalizing their electronic absorption and luminescence properties in both the basic and acid form. The latter are generated upon addition of trifluoroacetic acid to CH2Cl2 solutions of 1-9 and their formation is unambiguously evidenced by UV-vis absorption and 1H NMR spectroscopy. 1-9 can be subdivided into three groups, depending on their chemical structure and luminescence behavior. 1-3 are symmetrically substituted p-dianisylphenanthrolines which exhibit relatively intense violet fluorescence in CH2Cl2 (lambda(max) ca. 400 nm, Phi(fl) = 0.12-0.33) and are strongly quenched and substantially red-shifted upon protonation (lambda(max) ca. 550 nm, Phi(fl) = 0.010-0.045). 4-5 are 2,6-dimethoxyphenylphenanthrolines with faint luminescence in both the basic and acid form. 6-9 are various unsymmetric aryl-substituted-phenanthrolines and their relatively strong fluorescence (lambda(max) ca. 400 nm, Phi(fl) = 0.08-0.24) is red-shifted and substantially enhanced following protonation (lambda(max) ca. 475 nm, Phi(fl) = 0.16-0.50). The markedly different trends in the electronic absorption and fluorescence spectra are rationalized by means of both time-dependent Hartree-Fock and density functional theory by using hybrid functionals to assign the excited states. Interestingly, protonation of 1-9 also occurs in spin-coated films simply exposed to vapors of acid, and the reaction can be signaled by the color tuning of the emission signal (vapoluminescence). This observation makes substituted phenanthrolines potential candidates as proton sensors also in the solid phase.     

Proton and sodium cation affinities of harpagide: a computational study

The aim of this work was to estimate the proton and sodium cation affinities of harpagide (Har), an iridoid glycoside responsible for the antiinflammatory properties of the medicinal plant Harpagophytum. Monte Carlo conformational searches were performed at the semiempirical AM1 level to determine the most stable conformers for harpagide and its protonated and Na+-cationized forms. The 10 oxygen atoms of the molecule were considered as possible protonation and cationization sites. Geometry optimizations were then refined at the DFT B3LYP/6-31G level from the geometries of the most stable conformers found. Final energetics were obtained at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G level. The proton and sodium ion affinities of harpagide have been estimated at 223.5 and 66.0 kcal/mol, respectively. Since harpagide mainly provides HarNa+ ions in electrospray experiments, the DeltarG298 associated with the reaction of proton/sodium exchange between Har and methanol, MeOHNa+ + HarH+ --> MeOH2+ + HarNa+ (1), has been calculated; it has been estimated to be 1.9 kcal/mol. Complexing a methanol molecule to each reagent and product of reaction 1 makes the reaction become exothermic by 1.7 kcal/mol. These values are in the limit of the accuracy of the method and do not allow us to conclude definitely whether the reaction is endo- or exothermic, but, according to these very small values, the cation exchange reaction is expected to proceed easily in the final stages of the ion desolvation process.     

Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.     

Proton exchange and protonation of substituted oxadiazoles in trifluoroacetic acid

The rates of NH? COOH proton exchange between 5-amino-( 1a ) and 5-N-methylamino-( 1b )3-[2-(5′-nitro-2′-furyl)vinyl]-1,2,4-oxadiazoles and trifluoroacetic acid (TFA) have been measured by NMR spectroscopy. The values of the first-order rate constant and thermodynamic parameters for 1a and 1b , respectively, are: k_app (sec^?1) = 820 and 40 (50°C), ΔF (kcal/mole) = 14·7 and 16·5, ΔH^# (kcal/mole) = 17·3 and 24·3 and ΔS^# (e.u.) = 17 and 34. The comparison of rate constants indicates that after correction for proton equivalency proton exchange in 1a is faster than in 1b by a factor of ten. The presence of an NH₂ proton resonance ( 1a ) and an N-methyl doublet (J = 5·0 Hz) between 0 and 30° ( 1b ) suggests that 1a and 1b are present as amines and not as imines in TFA.     

Proton transfer in the hydrogen-bonded chains of lepidocrocite: a computational study

A responsible approach to the development of alternative energy sources, storage and conversion systems is to utilize abundant materials, with minimal or no negative environmental impacts. Here we report that lepidocrocite (γ-FeOOH, a naturally occurring metastable phase of iron oxyhydroxide) shows great promise as a proton conductor, based on sophisticated first-principles calculations that include the important corrections of on-site Coulomb interactions for this strongly correlated material. Our results show how proton transfer is facilitated by phonon vibration modes and relatively low transition energy barriers.     

Atypical protonation states in the active site of HIV-1 protease: a computational study

The HIV protease (HIVP) is a prominent example for successful structure-based drug design. Besides its pharmaceutical impact, it is a well-studied system for which, as experimentally evidenced, protonation changes in the active site occur upon ligand binding. Therefore, it serves as an ideal candidate for a case study using our newly developed partial charge model, which was optimized toward the application of Poisson-Boltzmann based pK(a) calculations. The charge model suggests reliably experimentally determined protonation states in the active site of HIVP. Furthermore, we perform pKa calculations for two HIVP complexes with novel types of inhibitors developed and synthesized in our group. For these complexes, no experimental knowledge about the protonation states is given. For one of the compounds, containing a central pyrrolidine ring, the calculations predict that both catalytic aspartates should be deprotonated upon ligand binding.     

Proton exchanges between phenols and ammonia or amines: a computational study

Density functional theory calculations at the B3LYP/6-31+G(d,p) level of theory have been performed to explore proton exchanges between phenols and ammonia or amines, which can be used to account for previous NMR experiments. For the parent phenol-NH(3) system, a transition state with a symmetric phenolate-NH(4)(+)-like structure, which lies about 35 kcal mol(-1) in energy above the hydrogen-bonded complex, has been successfully located. An intrinsic reaction coordinate (IRC) analysis indicates that the proton exchange is a concerted process, which can be roughly divided into four continuous subprocesses. A series of para-substituted phenol-NH(3) systems have been considered to investigate the substituent effect. Whereas introduction of an electron-withdrawing group on the phenol appreciably reduces the barrier, an opposite effect is observed for an electron-donating group. Moreover, it has been disclosed that there exists a good linear correlation between the activation barriers and the interaction energies between the phenols and NH(3), indicating the important role of proton transfer (or hydrogen bonding) in determining the proton exchange. Also considered are the proton exchanges between phenol and amines and those for some sterically hindered systems. The results show that the phenol tends to exchange hydrogen with the amines, preferably the secondary amines, and that the steric effect is favorable for the proton exchange, which imply that, as the IRC analysis suggested, besides the proton transfer, the flip of the ammonium-like moiety may play a significant role in the course of proton exchange. For all of these systems, we investigated the solvent effects and found that the barrier heights of proton exchange decrease remarkably as compared to those in a vacuum due to the ion pair feature of the transition state. Finally, we explored the phenol radical cation-NH(3) system; the barrierless proton transfer and remarkably low barrier (5.2 kcal mol(-1)) of proton exchange provide further evidence for the importance of proton transfer in the proton exchange.     

A theoretical study on the protonation of benzamide

We have performed an ab initio study of the protonation of benzamide, using a STO-3G minimal basis set. According to our results, benzamide is an oxygen-base in the gas-phase. Rotation of the -CONH₂ group respect to the aromatic ring does not affect the basicity of the molecule. If the presence of the solvent causes pyrimidization of the -NH₂ group, the intrinsic basicity of the O atom decreases, while that of the N atom increases and the interaction of this center with the solvent is stronger, favoring nitrogen protonation in solution.     

Corannulene as a Lewis base: computational modeling of protonation and lithium cation binding.

A computational modeling of the protonation of corannulene at B3LYP/6-311G(d,p)//B3LYP/6-311G(d,p) and of the binding of lithium cations to corannulene at B3LYP/6-311G(d,p)//B3LYP/6-31G(d,p) has been performed. A proton attaches preferentially to one carbon atom, forming a sigma-complex. The isomer protonated at the innermost (hub) carbon has the best total energy. Protonation at the outermost (rim) carbon and at the intermediate (bridgehead rim) carbon is less favorable by ca. 2 and 14 kcal mol(-)(1), respectively. Hydrogen-bridged isomers are transition states between the sigma-complexes; the corresponding activation energies vary from 10 to 26 kcal mol(-)(1). With an empirical correction obtained from calculations on benzene, naphthalene, and azulene, the best estimate for the proton affinity of corannulene is 203 kcal mol(-)(1). The lithium cation positions itself preferentially over a ring. There is a small energetic preference for the 6-ring over the 5-ring binding (up to 2 kcal mol(-)(1)) and of the convex face over the concave face (3-5 kcal mol(-)(1)). The Li-bridged complexes are transition states between the pi-face complexes. Movement of the Li(+) cation over either face is facile, and the activation energy does not exceed 6 kcal mol(-)(1) on the convex face and 2.2 kcal mol(-)(1) on the concave face. In contrast, the transition of Li(+) around the corannulene edge involves a high activation barrier (24 kcal mol(-)(1) with respect to the lowest energy pi-face complex). An easier concave/convex transformation and vice versa is the bowl-to-bowl inversion with an activation energy of 7-12 kcal mol(-)(1). The computed binding energy of Li(+) to corannulene is 44 kcal mol(-)(1). Calculations of the (7)Li NMR chemical shifts and nuclear independent chemical shifts (NICS) have been performed to analyze the aromaticity of the corannulene rings and its changes upon protonation.