Donor-acceptor interaction and intramolecular proton transfer in aminopolyenes

The influence of donor and acceptor substituents at chain termini on the geometry of the chain and charge distribution on atoms was studied for the ground and lower triplet electronically excited state of model ω-dimethylaminopolyene molecules (CH₃)₂N(CH=CH) _n CH=C(CN)₂, n = 1–3. Calculations were performed by the B3LYP/6-31+G** method. The influence of substituents on bond lengths and the amplitude of deviations from the equilibrium carbon-carbon bond length in unsubstituted polyenes increased as the conjugation chain grew longer. The deviations of the effects of both donor and acceptor groups from additivity, however, decreased. In the lower triplet electronically excited state of the molecule, the effect of substituents on changes in C-C bond lengths along the chain was not damped. The section of the potential energy surface for intramolecular proton shift from the donor amino to the acceptor nitrile group in “cyclic” (cis) conformers of the H₂N-CH=CH-CN and H₂N-CH=CH-CH=CH-CN molecules was analyzed. The structure of the reaction transition state and the height of the barrier to proton transfer were calculated.     

Influence of a polar near-neighbor on incipient proton transfer in a strongly hydrogen bonded complex

Rotational spectroscopy and ab initio calculations have been used to characterize the complexes H(3)N-HF and H(3)N-HF-HF in the gas phase. H(3)N-HF is a C(3v) symmetric, hydrogen bonded system with an NF distance of 2.640(21) A and an N...H hydrogen bond length of 1.693(42) A. The H(3)N-HF-HF complex, on the other hand, forms a six-membered HN-HF-HF ring, in which both the linear hydrogen bond in the H(3)N-HF moiety and the F-H-F angle of (HF)(2) are perturbed relative to those in the corresponding dimers. The N...F and F...F distances in the trimer are 2.4509(74) A and 2.651(11) A, respectively. The N...H hydrogen bond length in H(3)N-HF-HF is 1.488(12) A, a value which is 0.205(54) A shorter than that in H(3)N-HF. Similarly, the F...F distance, 2.651(11) A, is 0.13(2) A shorter than that in (HF)(2). Counterpoise-corrected geometry optimizations are presented, which are in good agreement with the experimental structures for both the dimer and trimer, and further characterize small, but significant, changes in the NH(3) and HF subunits upon complexation. Analysis of internal rotation in the spectrum of H(3)N-HF-HF gives the potential barrier for internal rotation of the NH(3) unit, V(3), to be 118(2) cm(-1). Ab initio calculations reproduce this number to within 10% if the monomer units and the molecular frame are allowed to fully relax as the internal rotation takes place. The binding energies of H(3)N-HF and H(3)N-HF-HF, calculated at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error are 12.3 and 22.0 kcal/mol, respectively. Additional energy calculations have been performed to explore the lowest frequency vibration of H(3)N-HF-HF, a ring-opening motion that increases the NFF angle. The addition of one HF molecule to H(3)N-HF represents the first step of microsolvation of a hydrogen bonded complex and the results of this study demonstrate that a single, polar near-neighbor has a significant influence on the extent of proton transfer across the hydrogen bond. As measured using the proton-transfer parameter rho(PT), previously defined by Kurnig and Scheiner [Int. J. Quantum Chem., Quantum Biol. Symp. 1987, 14, 47], the degree of proton transfer in H(3)N-HF-HF is greater than that in either (CH(3))(3)N-HF or H(3)N-HCl but less than that in (CH(3))(3)N-HCl.     

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.     

Intramolecular proton transfer

[structure: see text] Reversal of the normal kinetic protonation stereochemistry results as a consequence of intramolecular delivery.     

Dual fluorescence of ellipticine: excited state proton transfer from solvent versus solvent mediated intramolecular proton transfer

Photophysical properties of a natural plant alkaloid, ellipticine (5,11-dimethyl-6H-pyrido[4,3-b]carbazole), which comprises both proton donating and accepting sites, have been studied in different solvents using steady state and time-resolved fluorescence techniques primarily to understand the origin of dual fluorescence that this molecule exhibits in some specific alcoholic solvents. Ground and excited state calculations based on density functional theory have also been carried out to help interpretation of the experimental data. It is shown that the long-wavelength emission of the molecule is dependent on the hydrogen bond donating ability of the solvent, and in methanol, this emission band arises solely from an excited state reaction. However, in ethylene glycol, both ground and excited state reactions contribute to the long wavelength emission. The time-resolved fluorescence data of the system in methanol and ethylene glycol indicates the presence of two different hydrogen bonded species of ellipticine of which only one participates in the excited state reaction. The rate constant of the excited state reaction in these solvents is estimated to be around 4.2-8.0 × 10(8) s(-1). It appears that the present results are better understood in terms of solvent-mediated excited state intramolecular proton transfer reaction from the pyrrole nitrogen to the pyridine nitrogen leading to the formation of the tautomeric form of the molecule rather than excited state proton transfer from the solvents leading to the formation of the protonated form of ellipticine.     

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.     

Study of interaction of proton transfer probe 1-hydroxy-2-naphthaldehyde with serum albumins: a spectroscopic study

In the present work, we have studied the interaction of proton transfer probe 1-hydroxy-2-naphthaldehyde (HN12) with Human Serum Albumin (HSA) and Bovine Serum Albumin (BSA) by steady state absorption and emission spectroscopy combined with time resolved fluorescence measurements. The measured binding constant (K) and free energy change (DeltaG) indicate a stronger affinity of HN12 molecule for HSA than BSA. Steady state anisotropy, excitation anisotropy and fluorescence resonance energy transfer (FRET) studies indicate that the probe molecule resides at the hydrophobic site of the protein environment.     

Control of proton transfer: intramolecular vs intermolecular

[reaction: see text] Proton transfer in ketonization of enolates is a critical step in a myriad of organic reactions. Its stereochemistry has been the object of our studies since we reported kinetic protonation from the less hindered face of the molecule under kinetic control some decades ago. Very recently, we have succeeded in reversing the stereochemistry using 2-pyridyl groups to deliver the proton. We now report intramolecular delivery by other moieties and control of intramolecular versus intermolecular proton delivery.     

Hydrated alizarin complexes: hydrogen bonding and proton transfer

We investigated the hydrogen bonding structures and proton transfer for the hydration complexes of alizarin (Az) produced in a supersonic jet using fluorescence excitation (FE), dispersed laser induced fluorescence (LIF), visible-visible hole burning (HB), and fluorescence detected infrared (FDIR) spectroscopy. The FDIR spectrum of bare Az with two O-H groups exhibits two vibrational bands at 3092 and 3579 cm(-1), which, respectively, correspond to the stretching vibration of O1-H1 that forms a strong intramolecular hydrogen bond with the C9=O9 carbonyl group and the stretching vibration of O2-H2 that is weakly hydrogen-bonded to O1-H1. For the 1:1 hydration complex Az(H(2)O)(1), we identified three conformers. In the most stable conformer, the water molecule forms hydrogen bonds with the O1-H1 and O2-H2 groups of Az as a proton donor and proton acceptor, respectively. In the other conformers, the water binds to the C10=O10 group in two nearly isoenergetic configurations. In contrast to the sharp vibronic peaks in the FE spectra of Az and Az(H(2)O)(1), only broad, structureless absorption was observed for Az(H(2)O)(n) (n≥ 2), indicating a facile decay process, possibly due to proton transfer in the electronic excited state. The FDIR spectrum with the wavelength of the probe laser fixed at the broad band exhibited a broad vibrational band near the O2-H2 stretching vibration frequency of the most stable conformer of Az(H(2)O)(1). With the help of theoretical calculations, we suggest that the broad vibrational band may represent the occurrence of proton transfer by tunnelling in the electronic ground state of Az(H(2)O)(n) (n≥ 2) upon excitation of the O2-H2 vibration.     

Oxo-hydroxy tautomerism of 5-fluorouracil: water-assisted proton transfer

Post-Hartree-Fock ab initio quantum chemical calculations were performed for 5-fluorouracil in the gas phase and in a three-water cluster. Full geometry optimizations of the 5-fluorouracil-water complexes were carried out at the MP2/6-31+G(d,p) level of theory. MP4/6-31+G(d,p)//MP2/6-31+G(d,p) and MP4/6-31++G(d,p)//MP2/6-31+G(d,p) single-point calculations were performed to obtain more accurate energies. In water solution, 5-fluorouracil exists mainly in the 2,4-dioxo form (A). We propose that the populations of the 2-hydroxy-4-oxo (B) and 4-hydroxy-2-oxo (D) tautomers are 1 x 10(-4)% and 3.9 x 10(-8)%, respectively, on the basis of the relative stabilities of the tautomers calculated at the MP4/6-31++G(d,p)//MP2/6-31+G(d,p) level of theory. A profound difference between isolated and hydrated 5-fluorouracil is noted for the height of the tautomerization barrier. In the absence of water, the process of proton transfer is very slow. The addition of water molecules decreases the barrier by 2.3 times, making the process much faster. The minimum energy path (MP2/6-31+G(d,p)) for water-assisted proton transfer in trihydrated 5-fluorouracil was followed. CNDO/S-CI calculations predict singlet pi-pi(*) electron transitions at 312 nm for B and at 318 nm for D. The fluorescence spectrum of 5-fluorouracil in water confirms the presence of the hydroxy tautomer.     

Double proton transfer and charge transfer transitions in hydrogen-bonded systems: formic acid dimer

The barriers for double proton transfer in the ground and lowest Π-Π^* and Π-Π^* excited states of the formic acid dimer have been calculated within a modified INDO scheme. Analysis of the nature of the excited electronic states, with emphasis on charge-transfer transitions, has been performed. The results indicate a lower barrier in the excited Π-Π^* states than in the ground state.     

Dynamics of competitive reactions: endothermic proton transfer and exothermic substitution

Dynamics of an endothermic proton-transfer reaction, F(-) with dimethyl sulfoxide, and an endothermic proton-transfer reaction with a competing exothermic substitution (S(N)2) channel, F(-) with borane-methyl sulfide complex, were investigated using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR) and kinetic modeling. The two proton-transfer reactions have slightly positive and a small negative overall free energy changes, respectively. Energy-dependent rate constants were measured as a function of F(-) ion translational energy, and the resulting kinetics were modeled with the RRKM (Rice-Ramsperger-Kassel-Marcus) theory. The observed rate constants for the proton-transfer reactions of F(-) with dimethyl sulfoxide and with borane-methyl sulfide complex are identical, with a value of 0.17 x 10(-9) cm(3) molecule(-1) s(-1); for the S(N)2 reaction, k = 0.90 x 10(-9) cm(3) molecule(-1) s(-1) at 350 K. Both proton-transfer reactions have positive entropy changes in the forward direction and show positive energy dependences. The competing S(N)2 reaction exhibits negative energy dependence and becomes less important at higher energies. The changes of the observed rate constants agree with RRKM theory predictions for a few kcal/mol of additional kinetic energy. The dynamic change of the branching ratio for the competing proton transfer and the substitution reactions results from the competition between the microscopic rate constants associated with each channel.     

Excited-state intermolecular proton transfer of firefly luciferin V. Direct proton transfer to fluoride and other mild bases

We studied the direct proton transfer (PT) from electronically excited D-luciferin to several mild bases. The fluorescence up-conversion technique is used to measure the rise and decay of the fluorescence signals of the protonated and deprotonated species of D-luciferin. From a base concentration of 0.25 M or higher the proton transfer rates to the fluoride, dihdyrogen phosphate or acetate bases are fast and comparable. The fluorescence signals are nonexponential and complex. We suggest that the fastest decay component arises from a direct proton transfer process from the hydroxyl group of D-luciferin to the mild base. The proton donor and acceptor molecules form an ion pair prior to photoexcitation. Upon photoexcitation solvent rearrangement occurs on a 1 ps time-scale. The PT reaction time constant is ～2 ps for all three bases. A second decay component of about 10 ps is attributed to the proton transfer in a contact pair bridged by one water molecule. The longest decay component is due to both the excited-state proton transfer (ESPT) to the solvent and the diffusion-assisted PT process between a photoacid and a base pair positioned remotely from each other prior to photoexcitation.     

Dynamics of proton transfer in bacteriorhodopsin

Proton transfer in bacteriorhodopsin from the cytoplasm to the extracellular side is initiated from protonated asp96 in the cytoplasmic region toward the deprotonated Schiff base. This occurs in the transition from the photocycle late M state to the N state. To investigate this proton-transfer process, a quantum mechanics/molecular mechanics (QM/MM) model is constructed from the bacteriorhodopsin E204Q mutant crystal structure. Three residues, asp96, asp85, and thr89, as well as most of the retinal chromophore and the Schiff base link of lys216 are treated quantum mechanically and connected to the remaining classical protein through linker atom hydrogens. Structural transformation in the M state results in the formation of a water channel between the Schiff base and asp96. Since a part of this channel is lined with hydrophobic residues, there has been a question on the mechanism of proton transfer in a hydrophobic channel. Ab initio dynamics using the CHARMM/GAMESS methodology is used to simulate the transfer of the proton through a partially hydrophobic channel. Once sufficient water molecules are added to the channel to allow the formation of a single chain of waters from asp96 to the Schiff base, the transfer occurs as a fast (less than a picosecond) concerted event irrespective of the protonation state of asp85. Dynamic transfer of the proton from asp96 to the nearest water initiates the organization of a strongly bonded water chain conducive to the transfer of the proton to the Schiff base nitrogen.     

Electron and proton transfer in acid-base catalysis

The role of electron and proton transfer in acid-base catalysis is discussed, with two reactions as examples, in one of which (polymerization of cyclobutenes) an acid, and in another (nitramide decomposition), a base acts as the catalyst.     

Excited-state proton transfer kinetics of carbazole

Rate constants for the excited-state proton transfer reaction of carbazole in aqueous alkaline solution have been determined using picosecond single photon counting. Fluorescence decay measurements show that the back reaction is slow compared to the fluorescence decay time and therefore equilibrium is not attained in the excited state. The validity of a pK value for the lowest excited state determined from steady-state fluorescence measurements assuming equilibrium is discussed. It is concluded that the thermodynamic pK^* value for carbazole is 10.98.     

Anion-selective interaction and colorimeter by an optical metalloreceptor based on ruthenium(II) 2,2'-biimidazole: hydrogen bonding and proton transfer

A new anion sensor [Ru(bpy)2(H2biim)](PF6)2 (1) (bpy = 2,2'-bipyridine and H2biim = 2,2'-biimidazole) has been developed, in which the Ru(II)-bpy moiety acts as a chromophore and the H2biim ligand as an anion receptor via hydrogen bonding. A systematic investigation shows that 1 is an eligible sensor for various anions. It donates protons for hydrogen bonding to Cl-, Br-, I-, NO3-, HSO4-, H2PO4-, and OAc- anions and further actualizes monoproton transfer to the OAc- anion, changing color from yellow to orange brown. The fluoride ion has a high affinity toward the N-H group of the H2biim ligand for proton transfer, rather than hydrogen bonding, because of the formation of the highly stable HF2- anion, resulting in stepwise deprotonation of the two N-H fragments. These processes are signaled by vivid color changes from yellow to orange brown and then to violet because of second-sphere donor-acceptor interactions between Ru(II)-H2biim and the anions. The significant color changes can be distinguished visually. The processes are not only determined by the basicity of anion but also by the strength of hydrogen bonding and the stability of the anion-receptor complexes. The design strategy and remarkable photophysical properties of sensor 1 help to extend the development of anion sensors.     

Solid-state thiotropolone: an extremely rapid intramolecular proton transfer

Through variable-temperature solution-state NMR and molten- and solid-state CP/MAS (13)C NMR spectra, thiotropolone is found to exist as two rapidly equilibrated tautomeric structures, thione and enethiol, even in the solid state far below the melting point. The crystal structure shows an almost perpendicular packing, suggesting that the intramolecular hydrogen bond is dominant.