Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes.     

Polyglycine conformational analysis: calculated vs experimental gas-phase basicities and proton affinities

Structures of neutral and protonated polyglycines (Gly(n) and Gly(n)H(+) with n = 1-6) in the vicinity of global energy minima were calculated using the density functional theory at the B3LYP/6-311++G** (A) and B3LYP/6-31+G** (B) levels. Ninety-three structures were chosen for conformation and protonation studies. Geometries of the peptides are found to vary from open chains to multiple rings. Intramolecular hydrogen bonding is deduced to be the driving force for conformational stability. The preferred protonation sites are shown to be the terminal nitrogen atom and its adjacent amide oxygen atom. Structural series are developed according to geometrical form, hydrogen bonding, and protonation site. Physical factors that influence the relative electronic and thermodynamic stabilities of different structural series are examined. To obtain ab initio values of highest quality for gas-phase basicity (GB) and proton affinity (PA), electronic energies for n = 1-6 and thermal corrections to Gibbs free energy and enthalpy for n = 1-3 were calculated at level A, supplemented by thermal corrections for n = 4-6 at level B. Calculated GB and PA values are compared with mass spectral results obtained by the kinetic method (KM) and reaction bracketing (RB). The KM results and the ab initio values derived from structurally compatible pairs of lowest free energies are generally in good agreement, but the RB results for GB are lower by 2-8 kcal/mol for n = 2-6. Several reaction pathways are proposed to elucidate the experimental results. On the basis of theoretical structures consistent with the measurements, it is concluded that KM mostly samples the neutral and protonated structures of highest populations at thermal equilibrium, whereas RB targets those with sterically most accessible sites for protonation and deprotonation.     

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.     

Theoretical calculations of proton affinities of azines. Prediction of the relative basicities and preferred protonation sites

Theoretical calculations at the 3-21G and 3-21 + G ab initio levels and at the MNDO and AM1 semiempirical levels of several six-membered nitrogenated heterocycles and their protonated species have been carried out. The 3–21G calculated proton affinities are systematically too high, in relation to the available experimental data, and it is estimated that inclusion of electron correlation and zero-point corrections is not sufficient to reach the desired agreement; however, additional inclusion of diffuse functions (3-21 + G/3-21G calculations) lowers the calculated proton affinities by 5.4–6.8 kcal/mol, a good agreement being thus obtained, at least for 1–7 . On the other hand, semiempirical methods underestimate the repulsion between each pair of vicinal nitrogens; however, if a correction of ?9 kcal/mol is added to the AM1 results for each pair of neighboring nitrogens containing lone pairs of electrons, the corresponding proton affinities match fairly well the available exoerimental data and corrected 3-21 + G results. As expected, all methods predict that the introduction of additional nitrogens decreases the overall absolute basicity. Futhermore, comparison of the relative basicity of the isomers and of the preferred protonation site for each isomer indicates that nitrogen atoms with (only) one α-nitrogen and without a γ-nitrogen are more basic than any others. In benzazines, MNDO and AM1 suggest that the 2,3-diaza arrangement has a higher intrinsic basicity than the 1,2-diaza arrangement.     

Ab initio calculations and mass spectrometric determination of the gas-phase proton affinities of 4,4'-disubstituted 2,2'-bipyridines

The gas-phase proton affinities of 4,4'-di(R)-2,2'-bipyridines (R: H, Br, Cl, NO(2), Me) were determined by mass spectrometric measurements and by ab initio calculations at the HF/6-31G and MP2/6-31G levels of theory. The energy barriers for rotation about the central C-C bond were also studied computationally. Two minima were found for both unprotonated and protonated species, the global minima being at the trans planar and cis planar conformations, respectively. Local minima for the unprotonated compounds were at the cis nonplanar conformation and for the protonated compounds at the trans nonplanar. Two different proton affinity values were calculated for each compound by employing different conformations for the protonated species. The computational values were in good agreement with the experimental proton affinities. Substituents affect the proton affinity according to their ability to withdraw or to donate electrons, halogen and nitro-substituted bipyridines having a lower proton affinity and methyl-substituted bipyridine having a higher proton affinity than 2,2'-bipyridine itself.     

Atomistic and electronic structure of bimetallic cobalt/rhenium clusters from density functional theory calculations

We have carried out computational density functional investigations of Co I Re J (J=0,1,2; I+J=14) metal atom clusters. Through thorough optimization of geometry, spin polarization, and electronic configuration, the most stable structures for each cluster have been identified. While the global minima are found to be well defined and energetically well separated from other local minima, the study reveals a plethora of different structures and symmetries only moderately higher in energy. A key point of interest is the effect of doping the cobalt clusters with rhenium. Aside from significant structural reorganizations, rhenium is found to stabilize the clusters and couple down the spin. Furthermore, the most stable clusters comprise highly coordinated rhenium and, in the case of Co 12 Re 2, Re-Re bonding. Our results are compared to earlier experimental and computational data.     

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.     

Theoretical prediction of proton and electron affinities,gas phase basicities,and ionization energies of sulfinamides

Structural Chemistry - Sulfinamides, as an asymmetric synthesizer, especially in drug synthesis, play critical roles in organic chemistry. In this study, the gas phase ion energetics data including...     

Metal complexes of allyl derivatives of C60 fullerene: molecular and electronic structure prediction from density functional calculations

The problem of existence of ³—-complexes of C₆₀ fullerene with transition metal atoms is discussed. The complexes C₆₀R₃Co(CO)₃ (R = H, F, Cl, Br), C₆₀H₃NiCp, and C₆₀H₃Fe(CO)Cp, where C₆₀R₃ is an allyl derivative of C₆₀ fullerene, were shown to be sufficiently stable. In these complexes the metal atoms are ³—-bound to the fullerene cage. In contrast to this, the metal atoms in the C₆₀H₃Li and C₆₀H₃FeCp complexes are ⁵—-coordinated to the carbon cage. Density functional calculations were carried out with the Perdew—Burke—Ernzerhof exchange-correlation potential (PBE). It was concluded that the type of bonding in the complexes of allyl derivatives of C₆₀ fullerene depends on the nature of the species attached. Among the systems studied, the maximum energy of the ³—-bond was obtained for the C₆₀H₃NiCp complex. The results obtained can be useful in the design of synthesis of new fullerene derivatives with the ³—-coordination of the transition metal atoms to the carbon cage.     

Importance of gas-phase proton affinities in determining the electrospray ionization response for analytes and solvents

The effect of gas-phase proton transfer reactions on the mass spectral response of solvents and analytes with known gas-phase proton affinities was evaluated. Methanol, ethanol, propanol and water mixtures were employed to probe the effect of gas-phase proton transfer reactions on the abundance of protonated solvent ions. Ion-molecule reactions were carried out either in an atmospheric pressure electrospray ionization source or in the central quadrupole of a triple-quadrupole mass spectrometer. The introduction of solvent vapor with higher gas-phase proton affinity than the solvent being electrosprayed caused protons to transfer to the gas-phase solvent molecules. In mixed solvents, protonated solvent clusters of the solvent with higher gas-phase proton affinity dominated the resulting mass spectra. The effect of solvent gas-phase proton affinity on analyte response was also investigated, and the analyte response was suppressed or eliminated in solvents with gas-phase proton affinities higher than that of the analyte.     

An electronic structure perspective of the promoter modes in proton transfer reactions

The changes in the electronic structure are analyzed along the IRC of proton transfer reactions in two model systems, formic acid dimer and cyclic HF trimer. The IRC consists of three regions. In the first region, the two units between which a proton is exchanged approach each other. The vibrational mode associated with this movement is called the promoter mode. Computational evidence is provided to suggest that during this period the electrons in the lone pair of the acceptor atom delocalize significantly into the antibonding orbital of the covalent bond between the donor and hydrogen atoms. This reduces the barrier to the proton transfer. The force constants associated with the migrating protons also decrease as a result of the delocalization of lone pair electrons into the σ* orbital, and the associated stretching vibrational frequencies decrease along the IRC up to the transition state. In the second part of the IRC, the proton migration occurs. Finally, the two monomers retreat to the new equilibrium positions. On the basis of this, it is suggested that the role of the promoter mode is to enhance the flow of the lone pair electrons into the σ* orbital such that the barrier to the actual proton migration comes down. This can be used to identify them.     

Modeling proton transfer in imidazole-like dimers: a density functional theory study

A detailed theoretical study of proton transfer reaction in protonated imidazole, 1,2,3-triazole, and tetrazole dimers, the basic components of polymeric membrane used in proton exchange membranes fuel cells, has been carried out. In particular, several approaches based on density functional theory have been considered and their results compared with those provided by post-HF methods. From a computational point of view, these molecules appear to be a very challenging playground also for robust and recent functionals. Indeed none of the considered approaches provide results in close agreement with the reference post-HF data and a combined BMK//B3LYP model seems the only approach able to reproduce both the energetic and the structural features. From a chemical point of view, two new mechanisms of proton transfer in tetrazole dimers have been investigated and found to be more favorable than that previously hypothesized in literature. At the same time, the theoretical results show a direct connection between the obtained proton transfer barrier and the charge localized on the transferred hydrogen.     

Computation of interior eigenvalues in electronic structure calculations facilitated by density matrix purification

Density matrix purification, is in this work, used to facilitate the computation of eigenpairs around the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) in electronic structure calculations. The ability of purification to give large separation between eigenvalues close to the HOMO-LUMO gap is used to accelerate convergence of the Lanczos method. Illustrations indicate that a new eigenpair is found more often than every second Lanczos iteration when the proposed methods are used.     

Comparison of the orders of gas-phase basicities and ammonium ion affinities of polyethers by the kinetic method and ligand exchange technique

The orders of relative gas-phase basicities and ammonium ion affinities of a series of polyethers obtained by application of the kinetic method and ligand exchange technique are compared to evaluate the discrepancies of results between the two techniques. The order of gas-phase basicities determined by the ligand exchange technique in a quadrupole ion trap agrees with the order established previously by Kebarle using equilibrium methods in a high-pressure mass spectrometer. The order obtained by the kinetic method in a triple quadrupole mass spectrometer varies for the ranking of one polyether (12-crown-4), and this discrepancy is attributed to a difference in the rates of the competing dissociation pathways from the triethylene glycol dimethyl ether/12-crown4 proton-bound adduct, owing to a substantial variation in the flexibilities of these two ethers. For the order of gas-phase ammonium ion affinities, the kinetic method results agree overall with the ligand exchange results; however, the order of ammonium ion affinities for tetraethylene glycol dimethyl ether and 15-crown-5 could not be differentiated by the ligand exchange method because of the rapidity of ammonium ion transfer between the two polyethers in both directions.     

Parallel implementation of a mesh-based density functional electronic structure code

We describe the implementation of the mesh-based first-principles density functional code DMol on nCUBE 2 parallel computers. The numerical mesh nature of DMol makes it naturally suited for a massively parallel computational environment. Our parallelization strategy consists of a domain decomposition of mesh points. This evenly distributes mesh points to all available processors and leads to a substantial computational speedup with limited communication overhead and good node balancing. To achieve better performance and circumvent memory storage limitations, the torus wrap method is used to distribute both the Hamiltonian and overlap matrices, and a parallel matrix diagonalization routine is employed to calculate eigenvalues and eigenvectors. Benchmark calculations on a 128-node nCUBE 2 are presented. © 1995 by John Wiley & Sons, Inc.     

A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization

In this study, classic molecular dynamics (MD) simulations followed by density functional theory (DFT) calculations are employed to calculate the proton transfer reaction enthalpy shifts for native and derivatized peptide ions in the MALDI plume. First, absolute protonation and deprotonation enthalpies are calculated for native peptides (RPPGF and AFLDASR), the corresponding hexyl esters and three common matrices α-cyano-4-hydroxycinnamic acid (4HCCA), 2,5-dihydroxybenzoic acid (DHB), and 6 aza-2-thiothymine (ATT). From the proton exchange reaction calculations, protonation and deprotonation of the neutral peptides are thermodynamically favorable in the gas phase as long as the corresponding protonated/deprotonated matrix ions are present in the plume. Moreover, the gain in proton affinity shown by the ester ions suggests that the increase in ion yield is likely to be related to an easier proton transfer from the matrix to the peptide.     

A density functional theory study of dimers of hydrophosphoryl compounds and proton transfer in them

The structures of dimers of several types of dimethylphosphinous acid (CH₃)₂POH and dimethylphosphine oxide (CH₃)₂P(O)H and dimers of the corresponding perfluorinated derivatives (CF₃)₂POH and (CF₃)₂P(O)H were studied in detail by density functional theory with the PBE gradient-corrected functional and the TZ2p basis set. Fairly strong dimeric associates (2.50–10.5 kcal/mol) were shown to form thanks to O-H···O, O-H···P, and C-H···O H-bonds and dipole-dipole interactions of polar phosphoryl groups P → O of two monomer molecules. The existence of C-H···O and the absence of P-H···O H-bonds in (CH₃)₂P(O)H dimers was substantiated by an AIM (atoms in molecules) analysis of their structures according to Bader. The reaction coordinates were calculated for synchronous transfer of two protons in (CH₃)₂POH and (CF₃)₂P(O)H dimers. Both rearrangements were shown to occur via symmetrical six-membered planar transition states with activation barriers of less than 20 kcal/mol, which was much lower than for intramolecular transfer in the corresponding monomers (47 kcal/mol for the (CH₃)₂P(O)H → (CH₃)₂POH pair). The tautomeric transitions between the phosphinous acid and phosphine oxide forms observed experimentally in nonpolar media under mild conditions in the absence of molecules that could act as proton carriers were shown to proceed as bimolecular reactions with the intermediate formation of the corresponding dimers.