Calculation of proton transfers in hydrogen bonding interactions with semi-empirical MNDO/H

A method for calculating proton transfer enthalpies by a proper modification of the recent H-bonding version of MNDO is presented. This method perceives the proton as being both “bonded” and “hydrogen bonded” to the two electronegative atoms involved in the hydrogen bond: as it moves from one potential minimum at X-H---Y to the other at X---H-Y, a hydrogen bonding function is attached to the proportion of the distance that is to be traversed. The method is applied to two proton transfers within anionic oxygen H-bonded complexes and is shown to reduce the previously calculated barriers which were too high. Gas phase results for the single step of proton transfer over a barrier are required to evaluate the results obtained by this method.     

Analysis of ion binding on humic substances and the determination of intrinsic affinity distributions

Humic substances are characterized by a variable electric potential and by a variety of binding sites leading to chemical heterogeneity. Binding of ions to these substances is influenced by both factors. A methodology based on acid—base titrations at several salt levels is presented that allows for the assessment of an appropriate electrostatic double-layer model and the intrinsic proton affinity distribution. The double-layer model is used for the conversion of pH to pH_S for each data point, where H_S is the proton concentration in the diffuse layer near the binding site. It is shown that with an appropriate double-layer model the proton binding curves at different salt levels converge into one “master curve” when plotted as a function of pH_S. The intrinsic proton affinity distribution can then be derived from the “master curve” using the LOGA method. A rigorous analysis of metal binding to humic substances is complex and in practice is not feasible. Under two different (simplifying) assumptions, namely fully coupled and uncoupled binding, it is shown how intrinsic metal ion affinity distributions can be obtained. Model calculations show that apparent metal ion affinity distributions do not resemble the intrinsic metal ion affinity distribution.     

Einflüsse von substituenten in 6-stellung auf die 13C-chemischen verschiebungen der kohlenstoffatome des purins

The ¹³C chemical shifts of purines substituted in the 6 position are reported. Signals are assigned on the basis of general chemical shift rules and by proton “off-resonance” decoupling. Substituent effects (Z_6i) of the substituent X in the 6 position of purine on the ¹³C chemical shifts of purine ring carbon atoms are determined. A linear correlation exists between the substituent effects of X on C-6 (Z₆₆) and Pauling's electronegativity values E_x of the substituent X.     

Incorporating solvation effects into density functional theory: Calculation of absolute acidities

An approach to the calculation of molecular electronic structures, solvation energies, and pK_a values in condensed phases is described. The electronic structure of the solute is described by density functional quantum mechanics, and electrostatic features of environmental effects are modeled through external charge distributions and continuum dielectrics. The reaction potential produced by a mode of the molecular charge distribution is computed via finite-difference solutions to the Poisson-Boltzmann equation and incorporated into the self-consistent field procedure. Here we report results on three sets of organic acids, whose pK_a values range over 16 pH units. The first set provides models for ionizable side chains in proteins; the second set considers the effects of substituting one to three chlorine atoms for hydrogens in acetic acid; and the final set consists of 4-substituted-bicyclo-[2.2.2]-octanecarboxylic acids. Successful prediction of “absolute” pK_a values places stringent requirements on the computation of gas-phase proton affinities and on the response to solvation. In some cases the current model shows substantial errors, but overall the results and trends are in good agreement with experiment. Prospects for extending this approach to more complex systems such as proteins are briefly discussed. © 1997 John Wiley & Sons, Inc.     

Periodicity in proton conduction along a H‐bonded chain. Application to biomolecules

Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H⁺)? H₂O? CH₃COO^? model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H‐bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H‐bond lengths and the progression of proton transfer in each link. This “wave” is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Solvent effects and specific interactions in I.R. absorption spectra of 2- and 4- pyrimidinones

Infrared spectra of 2- and 4- pyrimidinone solutions in acetonitrile-water mixtures have been recorded in order to assign the fundamental bands and study solvent effects. It was found absorption bands change with increasing water concentration. The CO “free” absorption band decreases, while the CO associated increases. This may be attributed to intermolecular hydrogen bonding between the CO group of 2- and 4- pyrimidinones and water; both compounds act as proton acceptors, while water behaves as a proton donor. The equilibrium constant and the stoichiometry of hydrogen-bond formation have been determined by means of some equations which are discussed.     

Light-Induced Structural Changes in the Primary Processes of Photosynthesis: Watching an Enzyme in Action

Continuous illumination and subsequent freezing of the crystal enabled the structure of the light-induced charge-separated state in the reaction center of a photosynthetic bacterium to be obtained by X-ray crystallography. A comparison of the position of the secondary ubiquinone cofactor Q_B in this structure (shown in gray on the right) with that in the “dark” structure (shown in black) reveals substantial motions, which are required for the subsequent electron and proton transfer processes.     

The Protoelectric Potential Map (PPM): An Absolute Two‐Dimensional Chemical Potential Scale for a Global Understanding of Chemistry

We introduce the protoelectric potential map (PPM) as a novel, two‐dimensional plot of the absolute reduction potential (pe_abs scale) combined with the absolute protochemical potential (Brønsted acidity: pH_abs scale). The validity of this thermodynamically derived PPM is solvent‐independent due to the scale zero points, which were chosen as the ideal electron gas and the ideal proton gas at standard conditions. To tie a chemical environment to these reference states, the standard Gibbs energies for the transfer of the gaseous electrons/protons to the medium are needed as anchor points. Thereby, the thermodynamics of any redox, acid–base or combined system in any medium can be related to any other, resulting in a predictability of reactions even over different media or phase boundaries. Instruction is given on how to construct the PPM from the anchor points derived and tabulated with this work. Since efforts to establish “absolute” reduction potential scales and also “absolute” pH scales already exist, a short review in this field is given and brought into relation to the PPM. Some comments on the electrochemical validation and realization conclude this concept article.     

Estimating local bonding/antibonding character of canonical molecular orbitals from their energy derivatives. The case of coordinating lone pair orbitals

According to Koopmans theorem, the derivative of the energy of a canonical molecular orbital (MO) with respect to nuclear coordinates quantifies its bonding/antibonding character. This quantity allows predictions of bond length variation on ionisation in a panel of 19 diatomic species. In polyatomic molecules, the derivative of a MO energy with respect to a given bond length reveals the nature and the degree of the bonding/antibonding contribution of this MO with respect to this bond. Accordingly, the HOMO “lone pairs” of CO and CN^? and the HOMO‐2 of CH₃CN are found to be antibonding with respect to the C? X bond (X = N, O), whereas the HOMO of N₂ is found to be bonding. With the same approach, the variation of the bonding character in the MOs of CO and CH₃CN on interaction with an electron acceptor (modeled through the approach of a proton) or by applying an electric field was studied. © 2016 Wiley Periodicals, Inc.     

The “Inverted Bonds” Revisited: Analysis of “In Silico” Models and of [1.1.1]Propellane by Using Orbital Forces

This article dwells on the nature of “inverted bonds”, which refer to the σ interaction between two sp hybrids by their smaller lobes, and their presence in [1.1.1]propellane. Firstly, we study H₃C−C models of C−C bonds with frozen H-C-C angles reproducing the constraints of various degrees of “inversion”. Secondly, the molecular orbital (MO) properties of [1.1.1]propellane and [1.1.1]bicyclopentane are analyzed with the help of orbital forces as a criterion of bonding/antibonding character and as a basis to evaluate bond energies. Triplet and cationic states of [1.1.1]propellane species are also considered to confirm the bonding/antibonding character of MOs in the parent molecule. These approaches show an essentially non-bonding character of the σ central C−C interaction in propellane. Within the MO theory, this bonding is thus only due to π-type MOs (also called “banana” MOs or “bridge” MOs) and its total energy is evaluated to approximately 50 kcal mol⁻¹. In bicyclopentane, despite a strong σ-type repulsion, a weak bonding (15–20 kcal mol⁻¹) exists between both central C−C bonds, also due to π-type interactions, though no bond is present in the Lewis structure. Overall, the so-called “inverted” bond, as resulting from a σ overlap of the two sp hybrids by their smaller lobes, appears highly questionable.     

Correlation effects on energy curves for proton transfer. The cation [H5O2]+

Potential curves for proton transfer in [H₅O₂]⁺ and for the dissociation of one OH bond in [H₃O]⁺ were calculated by both ab initio and semi-empirical LCAO MO SCF CI methods. The energy barrier of the symmetric double minimum potential in [H₅O₂]⁺ is very sensitive to electron correlation. At an OO distance of 2.74 Å it decreases from the HF value of 9.5 kcal/mole to about 7.0 kcal/mole. The results of the semi-empirical calculations agree well with the ab initio data as long as only relative effects are regarded. The partitioning of correlation energy into contributions of individual electron pairs is very similar for proton transfer in [H₅O₂]⁺ and for the dissociation of one OH bond in [H₃O]⁺. In this example the proton transfer appears as a superposition of two “contracted ionic dissociation” processes. An interpretation of the behaviour of correlation during these processes is presented.     

The Role of Molecular Electrostatic Potentials in the Formation of a Halogen Bond in Furan⋅⋅⋅XY and Thiophene⋅⋅⋅XY Complexes

The halogen bonding of furan???XY and thiophene???XY (X=Cl, Br; Y=F, Cl, Br), involving σ‐ and π‐type interactions, was studied by using MP2 calculations and quantum theory of “atoms in molecules” (QTAIM) studies. The negative electrostatic potentials of furan and thiophene, as well as the most positive electrostatic potential (V_S,max) on the surface of the interacting X atom determined the geometries of the complexes. Linear relationships were found between interaction energy and V_S,max of the X atom, indicating that electrostatic interactions play an important role in these halogen‐bonding interactions. The halogen‐bonding interactions in furan???XY and thiophene???XY are weak, “closed‐shell” noncovalent interactions. The linear relationship of topological properties, energy properties, and the integration of interatomic surfaces versus V_S,max of atom X demonstrate the importance of the positive σ hole, as reflected by the computed V_S,max of atom X, in determining the topological properties of the halogen bonds.     

New Tris(hydroxypyridinones) as Iron and Aluminium Sequestering Agents: Synthesis,Complexation and In Vivo Studies

Two new tripodal tris(3‐hydroxy‐4‐pyridinone) hexadentate chelators—NTA(BuHP)₃ and NTP(PrHP)₃ (NTA=nitrilotriacetic acid, NTP=nitrilotripropionic acid, HP=hydroxypyridone)—have been developed and studied in solution for their iron and aluminium binding affinity, and also assayed in vivo for their capacity to remove metal from an animal model that is overloaded. These chelators are positional isomers, possessing identical general structures based on aminotricarboxylic acid skeletons attached to three bidentate 3‐hydroxy‐4‐pyridinones (3,4‐HPs), but differing in the position of the amide linkage along the chelating “arm”. In spite of expected differences in the tripodal ligands, such as acidity and hydrogen‐bonding networks, they share important properties, namely, a mild hydrophilic character (log P ca. ?1.2 to ?1.4) and a strong chelating affinity for Fe and Al (pFe=27.9 and pAl=22.0 for NTA(BuHP)₃; pFe=29.4 and pAl=22.4 for NTP(PrHP)₃). They also evidenced identical effects on the biodistribution and on the excretion of a radiotracer (⁶⁷Ga) previously administered to mice, as models of iron overload animals. Comparison of the new compounds with reported analogues shows good improvement in terms of solution and in vivo sequestering properties, thus giving support to expectations about their potential clinical application as metal removal agents.     

Theoretical insights into the excited‐state process of 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol

In this paper, we theoretically explore the motivation and behaviors of the excited‐state intramolecular proton transfer (ESIPT) reaction for a novel white organic light‐emitting diode (WOLED) material 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol (t‐MTTH). The “atoms in molecules” (AIM) method is adopted to verify the formation and existence of the hydrogen bond O? H···N. By analyzing the excited‐state hydrogen bonding behaviors via changes in the chemical bonding and infrared (IR) vibrational spectra, we confirm that the intramolecular hydrogen bond O? H···N should be getting strengthened in the first excited state in four kinds of solvents, thus revealing the tendency of ESIPT reaction. Further, the role of charge‐transfer interaction is addressed under the frontier molecular orbitals (MOs), which depicts the nature of the electronic excited state and supports the ESIPT reaction. Also, the electron distribution confirms the ESIPT tendency once again. The scanned and optimized potential energy curves according to variational O? H coordinate in the solvents demonstrate that the proton transfer reaction should occur in the S₁ state, and the potential energy barriers along with ESIPT direction support this reaction. Based on the excited‐state behaviors reported in this work, the experimental spectral phenomenon has been reasonably explained.     

A valence bond study of the oxygen molecule

Ab initio valence bond calculations are performed for the three lowest states of the oxygen molecule (³Σ⁻_g, ¹Δ_g, and ¹Σ⁺_g). One objective of the present study was to make a contribution to previous valence bond discussions about the oxygen “double” bond. Further, we study the origin of a small barrier in the potential energy surface of the ground state. Two compact models are employed to maintain the clear picture that can be offered by the valence bond method. The first model has only the Rumer structures that are essential for bonding and a proper dissociation. The second model, in addition, has structures which represent excited atoms. These prove to be important for the dissociation energies. For both models, the orbitals are fully optimized. The spectroscopic data obtained are significantly better than are the (few) valence bond results on O₂ that have been published and have the quality of multiconfiguration self-consistent field calculations in which the same valence space is used. The “hump” in the potential energy surface of the ground state is shown to arise from a spin recoupling. The free atoms correspond to a spin coupling that is incapable of describing the formation of bonds. Only at short distances, an alternative spin coupling provides bonding and the repulsive curve is converted into an attractive one. Our results on this subject support a valence bond explanation previously given by McWeeny [R. McWeeny, Int. J. Quantum Chem. Symp. 24 , 733 (1990)]. © 1996 John Wiley & Sons, Inc.     

Nature‐Inspired Environmental “Phosphorylation” Boosts Photocatalytic H2 Production over Carbon Nitride Nanosheets under Visible‐Light Irradiation

Inspired by the crucial roles of phosphates in natural photosynthesis, we explored an environmental “phosphorylation” strategy for boosting photocatalytic H₂ production over g‐C₃N₄ nanosheets under visible light. As expected, a substantial improvement was observed in the rate of H₂ evolution to 947 μmol h^?1, and the apparent quantum yield was as high as 26.1 % at 420 nm. The synergy of enhanced proton reduction and improved hole oxidation is proposed to account for the markedly increased activity. Our findings may provide a promising and facile approach to highly efficient photocatalysis for solar‐energy conversion.     

Intramolecular single and double proton transfer in benzoxazole derivatives

The “double” derivatives of benzoxazole, bis-2,5-(2-benzoxazolyl)hydroquinone (II) and bis-3,6-(2-benzoxazolyl)-pyrocatochol (III), have been investigated. In (II), only one proton is transferred in the S₁ state. Primary and tautomeric forms exist in a rapidly established equilibrium. In (III), two tautomers were detected. One is generated in the S₁ state by a double proton transfer without a potential barrier, while the other, generated by a single proton transfer, is already present in trace amounts in the S₀ state.