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     

An electron density based analysis to establish the electronic adiabaticity of proton coupled electron transfer reactions

Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems.     

TD‐DFT study on the sensing mechanism of a fluorescent chemosensor for fluoride: Excited‐state proton transfer

An excited‐state proton transfer (ESPT) process, induced by both intermolecular and intramolecular hydrogen‐bonding interactions, is proposed to account for the fluorescence sensing mechanism of a fluoride chemosensor, phenyl‐1H‐anthra(1,2‐d)imidazole‐6,11‐dione. The time‐dependent density functional theory (TD‐DFT) method has been applied to investigate the different electronic states. The present theoretical study of this chemosensor, as well as its anion and fluoride complex, has been conducted with a view to monitoring its structural and photophysical properties. The proton of the chemosensor can shift to fluoride in the ground state but transfers from the proton donor (NH group) to a proton acceptor (neighboring carbonyl group) in the first singlet excited state. This may explain the observed red shifts in the fluorescence spectra in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

A TD‐DFT study on the cyanide‐chemosensing mechanism of 8‐formyl‐7‐hydroxycoumarin

Proton transfer (PT) and excited‐state PT process are proposed to account for the fluorescent sensing mechanism of a cyanide chemosensor, 8‐formyl‐7‐hydroxycoumarin. The time‐dependent density functional theory method has been applied to investigate the ground and the first singlet excited electronic states of this chemosensor as well as its nucleophilic addition product with cyanide, with a view to monitoring their geometries and spectrophotometrical properties. The present theoretical study indicates that phenol proton of the chemosensor transfers to the formyl group along the intramolecular hydrogen bond in the first singlet excited state. Correspondingly, the nucleophilic addition product undergoes a PT process in the ground state, and shows a similar structure in the first singlet excited state. This could explain the observed strong fluorescence upon the addition of the cyanide anion in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

A detailed theoretical study on the excited‐state hydrogen‐bonding dynamics and the proton transfer mechanism for a novel white‐light fluorophore

In this work, density functional theory (DFT) and time‐dependent DFT (TDDFT) methods were used to investigate the excited‐state dynamics of the excited‐state hydrogen‐bonding variations and proton transfer mechanism for a novel white‐light fluorophore 2‐(4‐[dimethylamino]phenyl)‐7‐hyroxy‐6‐(3‐phenylpropanoyl)‐4H‐chromen‐4‐one ( 1 ). The methods we adopted could successfully reproduce the experimental electronic spectra, which shows the appropriateness of the theoretical level in this work. Using molecular electrostatic potential (MEP) as well as the reduced density gradient (RDG) versus the product of the sign of the second largest eigenvalue of the electron density Hessian matrix and electron density (sign[λ₂]ρ), we demonstrate that an intramolecular hydrogen bond O1–H2···O3 should be formed spontaneously in the S₀ state. By analyzing the chemical structures, infrared vibrational spectra, and hydrogen‐bonding energies, we confirm that O1–H2·O3 should be strengthened in the S₁ state, which reveals the possibility of an excited‐state intramolecular proton transfer (ESIPT) process. On investigating the excitation process, we find the S₀ → S₁ transition corresponding to the charge transfer, which provides the driving force for ESIPT. By constructing the potential energy curves, we show that the ESIPT reaction results in a dynamic equilibrium in the S₁ state between the forward and backward processes, which facilitates the emission of white light.     

Cooperativity and proton transfer in hydrogen-bonded triads.

Ab initio MP2/6-311+G(3df,2pd) and MP2/aug-cc-pVTZ calculations have been carried out to investigate the structures and properties of AHXHYH(3) (A=F, Cl; X=F, Cl; Y=N, P) hydrogen-bonded complexes. Significant cooperative effects are observed in the XHYH3 dyads in the triads due to the presence of the polar near-neighbor AH. These effects are greater when the polar partner is HF, which is a better proton donor than HCl. Structural changes, red shifts of proton-donor stretching frequencies, nonadditive interaction energies, and electron density redistributions unambiguously demonstrate that the X--HY hydrogen bond (HB) is stronger in the triads than in the corresponding dyads, while the X--H bond of the proton donor becomes weaker. Even more pronounced cooperative effects are observed in the AHXH dyads due to the presence of the YH3 partner. These effects are weaker in complexes having PH3 rather than NH3 as the proton acceptor, since NH3 is a stronger base. Cooperativity also enhances the proton-donating ability of the YH3 moiety, with the result that all complexes except FHFHPH3 are cyclic. Cooperativity, together with the ease of breaking the Cl--H bond in ClHClHNH3 and FHClHNH3, leads to proton transfer (PT), so that these two complexes are better described as approaching hydrogen-bonded ClHCl- x +HNH3 and FHCl- x +HNH3 ion pairs.     

A Computational Study of the Mechanism of Hydrogen Evolution by Cobalt(Diimine‐Dioxime) Catalysts

Cobalt(diimine‐dioxime) complexes catalyze hydrogen evolution with low overpotentials and remarkable stability. In this study, DFT calculations were used to investigate their catalytic mechanism, to demonstrate that the initial active state was a Co^I complex and that H₂ was evolved in a heterolytic manner through the protonation of a Co^II? hydride intermediate. In addition, these catalysts were shown to adjust their electrocatalytic potential for hydrogen evolution to the pH value of the solution and such a property was assigned to the presence of a H⁺‐exchange site on the oxime bridge. It was possible to establish that protonation of the bridge was directly involved in the H₂‐evolution mechanism through proton‐coupled electron‐transfer steps. A consistent mechanistic scheme is proposed that fits the experimentally determined electrocatalytic and electrochemical potentials of cobalt(diimine‐dioxime) complexes and reproduces the observed positive shift of the electrocatalytic potential with increasing acidity of the proton source.     

A theoretical study on the excited‐state intramolecular proton transfer mechanism of 4′‐dimethylaminoflavonol chemosensor

In this work, density functional theory (DFT) and time‐dependent density functional theory (TDDFT) methods are used to explore the excited‐state intramolecular proton transfer (ESIPT) mechanism of a novel system 4′‐dimethylaminoflavonol (DAF). By analyzing the molecular electrostatic potential (MEP) surface, we verify that the intramolecular hydrogen bond in DAF exists in both the S₀ and S₁ states. We calculate the absorption and emission spectra of DAF in two solvents, which reproduce the experimental results. By comparing the bond lengths, bond angles, and relative infrared (IR) vibrational spectra involved in the hydrogen bonding of DAF, we confirm the hydrogen‐bond strengthening in the S₁ state. For further exploring the photoexcitation, we use frontier molecular orbitals to analyze the charge redistribution properties, which indicate that the charge transfer in the hydrogen‐bond moiety may be facilitating the ESIPT process. The constructed potential energy curves in acetonitrile and methylcyclohexane solvents with shortened hydrogen bond distances demonstrate that proton transfer is more likely to occur in the S₁ state due to the lower potential barrier. Comparing the results in the two solvents, we find that aprotic polar and nonpolar solvents seem to play similar roles. This work not only clarifies the excited‐state behaviors of the DAF system but also successfully explains its spectral characteristics.     

Theoretical study of the reaction mechanism of proton transfer in glycinamide

To investigate the tautomerism of glycinamide that is induced by proton transfer, we present detailed theoretical studies on the reaction mechanism of both the isolated gas phase and H₂O‐assisted proton transfer process of glycinamide, using density functional theory calculations by means of the B3LYP hybrid functional. Twenty‐six geometries, including 10 significant transition states, were optimized, and these geometrical parameters are discussed in detail. The relative order of the activation energy for hydrogen atom transfer of all the conformers has been systematically explored in this essay. For the amido hydrogen atom transfer process, the relative order of the activation energy is: IV < II < III < I, while in the carbonic hydrogen atom transfer process, the relative order is IV > II > III > I. Meanwhile, the most favorable structure for both the amido hydrogen atom transfer and the carbonic hydrogen atom transfer has been found. The involvement of the water molecule not only can stabilize the transition states and the ground states, but can also reduce the activation energy greatly. The superior catalytic effect of H₂O has been discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical exploration about excited state proton transfer mechanism for a series of phenol–quinoline compounds

In the present work, three novel phenols (10a,11‐dihydro‐4bH‐indeno[1,2‐b]quinolin‐4‐ol ( 1 ), 5,6‐dihydro‐benzo[c]acridin‐1‐ol ( 2 ), and 5,5,7,7a‐tetrahydro‐4aH‐13‐aza‐benzo[3,4]cyclohepta[1,2‐b]naphthalene‐1‐ol ( 3 )) have been explored theoretically in detail. Using density functional theory (DFT) and time‐dependent DFT (TDDFT) methods, we inquire into the intramolecular hydrogen‐bonding interactions and the excited‐state intramolecular proton transfer (ESIPT) process. Exploring the steady‐state absorption and emission spectra under TDDFT/B3LYP/TZVP theoretical level in acetonitrile solvent, our calculated results demonstrate an experimental phenomenon. Based on analysis of the variations of geometrical parameters and infrared (IR) vibrational spectra, we confirm that O–H?N should be strengthened in the S₁ state. Investigating the frontier molecular orbitals (MOs) and the charge density difference (CDD) maps, it can be confirmed that the charge redistribution facilitates the tendency of the ESIPT process for 1 , 2, and 3 systems. By constructing potential energy curves, we confirm that the proton transfer should occur in the S₁ state. In particular, the ESIPT for 2 and 3 systems are nonbarrier processes in the S₁ state, which confirms that ESIPT should be exothermal spontaneously. This work explains previous experimental results and makes a reasonable assumption about the ESIPT mechanism for 1 , 2 and 3 systems. We sincerely hope our work can facilitate understanding and promoting applications about them in future.     

Interesting properties of Thomas–Fermi kinetic and Parr electron–electron‐repulsion DFT energy functional generated compact one‐electron density approximation for ground‐state electronic energy of molecular systems

The reduction of the electronic Schrodinger equation or its calculating algorithm from 4N‐dimensions to a (nonlinear, approximate) density functional of three spatial dimension one‐electron density for an N‐electron system, which is tractable in the practice, is a long desired goal in electronic structure calculation. If the Thomas‐Fermi kinetic energy (～∫ρ^5/3d r ₁) and Parr electron–electron repulsion energy (～∫ρ^4/3d r ₁) main‐term functionals are accepted, and they should, the later described, compact one‐electron density approximation for calculating ground state electronic energy from the 2nd Hohenberg–Kohn theorem is also noticeable, because it is a certain consequence of the aforementioned two basic functionals. Its two parameters have been fitted to neutral and ionic atoms, which are transferable to molecules when one uses it for estimating ground‐state electronic energy. The convergence is proportional to the number of nuclei (M) needing low disc space usage and numerical integration. Its properties are discussed and compared with known ab initio methods, and for energy differences (here atomic ionization potentials) it is comparable or sometimes gives better result than those. It does not reach the chemical accuracy for total electronic energy, but beside its amusing simplicity, it is interesting in theoretical point of view, and can serve as generator function for more accurate one‐electron density models. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.     

Correlation energy,correlated electron density,and exchange‐correlation potential in some spherically confined atoms

We report correlation energies, electron densities, and exchange‐correlation potentials obtained from configuration interaction and density functional calculations on spherically confined He, Be, Be²⁺, and Ne atoms. The variation of the correlation energy with the confinement radius R_c is relatively small for the He, Be²⁺, and Ne systems. Curiously, the Lee–Yang–Parr (LYP) functional works well for weak confinements but fails completely for small R_c. However, in the neutral beryllium atom the CI correlation energy increases markedly with decreasing R_c. This effect is less pronounced at the density‐functional theory level. The LYP functional performs very well for the unconfined Be atom, but fails badly for small R_c. The standard exchange‐correlation potentials exhibit significant deviation from the “exact” potential obtained by inversion of Kohn–Sham equation. The LYP correlation potential behaves erratically at strong confinements. © 2016 Wiley Periodicals, Inc.     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

细菌紫红质中氢键相互作用和质子转移机理的分子模拟

用CHARMM程序以细菌紫红质1R84晶体为模型, 模拟了在等温定容条件下细菌紫红质在1 ps过程中的变化, 分析了与质子传递相关的ASP85, ASP212和水分子与视黄醛间氢键的结构变化情况. 考虑到氨基酸残基和席夫碱质子的不同距离, 考察了EC和PC两种结构的变化情况, 探讨了紫红质中质子传递的可能途径. 模拟结果表明1R84中可能的质子连续传递的机理是质子由席夫碱向水传递, 再由水向ASP85传递. 发现Asp212在模拟过程中保持EC结构, 这样可能更有利于顺序质子传递.