Double Proton Transfer Research Articles

A Computational Study on Reduction Mechanism of Silver Nanoparticles Synthesis

Abstract The redox reaction pathway of silver nanocluster formation in the polyol method is investigated by density functional theory calculation. It is suggested that the formation of Ag2(0) cluster with silver acetate dimer and glycol is more likely to occur via the Ag–carbon bond intermediate rather than via concerted double proton transfer or Ag-alkoxide intermediate. The aldehyde produced from glycol acts as a stronger reducing agent in the reaction. This mechanism provides important insights for controlling the reaction of the polyol process.

Double proton transfer in a polar nano-droplet: Phototautomerization of alloxazine in AOT/alkane reverse micelles containing water or glycerol

Alloxazine phototautomerization is believed to occur through an excited state double proton transfer (ESDPT) mechanism involving cyclic intermolecular H-bonded complexes between Alloxazine and hydroxylic solvents like water and alcohols. In AOT/alkane dispersions in the absence of any polar liquid, Alloxazine molecules reside inside the polar core of the AOT reverse micelle nanoparticles, where they involve in H-bonding with the anionic sulfonate head-groups of the AOT molecules, but are unable to generate the appropriate cyclic intermolecular H-bonded complexes conducive to ESDPT. However, tautomerization is switched on with addition of water and formation ofwater nano-droplet at the core of reverse micelle. Evidently, the Alloxazine⋅⋅⋅⋅AOT H-bonds are now replaced by Alloxazine⋅⋅⋅⋅Water H-bonds, promotingESDPT. On the other hand, Alloxazine phototautomerization is hindered in Glycerol, irrespective of whether the latter is in the bulk liquid state or in the form of a polar nano-droplet. This may be explained by steric considerations.

Excited-State Intramolecular Proton Transfer: A Short Introductory Review.

In this short review, we attempt to unfold various aspects of excited-state intramolecular proton transfer (ESIPT) from the studies that are available up to date. Since Weller’s discovery of ESIPT in salicylic acid (SA) and its derivative methyl salicylate (MS), numerous studies have emerged on the topic and it has become an attractive field of research because of its manifold applications. Here, we discuss some critical aspects of ESIPT and tautomerization from the mechanistic viewpoint. We address excitation wavelength dependence, anti-Kasha ESIPT, fast and slow ESIPT, reversibility and irreversibility of ESIPT, hydrogen bonding and geometrical factors, excited-state double proton transfer (ESDPT), concerted and stepwise ESDPT.

Searching for a near-infrared fluorescence band supporting a hypothetical double proton transfer in ESIPT reaction of 2,5-bis(2′-benzoxazolyl) hydroquinone (BBHQ), as requested by theoreticians

New near-infrared broad-band emission with λmax~920 nm was detected in 2,5-bis(2′-benzoxazolyl)hydroquinone (BBHQ), a molecule known to undergo the single proton transfer in the ESIPT reaction and to emit the fluorescence with λmax ~600 nm. The new emission was attributed to the fluorescence of the product of double proton transfer in the excited BBHQ. The attribution was based on the qualitative agreement verifying the theoretical predictions and on the behaviour of the two properly chosen derivatives: the diethyl-BBHQ independently showing the same broad-band IR fluorescence, and the monomethoxy-BBHQ, a “negative witness”- a structure with one of two ESIPT reactivity sites eliminated, showing no trace of the new emission.

Molecular Dynamics Characterization of Dielectron Hydration in Liquid Water with Unique Double Proton Transfers.

Radiation chemistry of water and aqueous solutions has always been an interesting scientific issue owing to involving electronic excitations, ionization of solvated species, and formation of radiolytic species and many elementary reactions, but the underlying mechanisms are still poorly understood. Here, we for the first time molecular dynamics characterize the hydration dynamics of two correlated electrons and their triggered unique phenomena in liquid water associated with radiolysis of water using the combined hybrid functional and nonlocal dispersion functional. Hydration of two electrons may experience two distinctly different mechanisms, one forming a spin-paired closed-shell unicaged dielectron hydrate (e22-aq) and the other forming a spin-paired metastable open-shell bicaged hydrated electron pair (e-aq···e-aq) which exhibits intriguing antiferromagnetic spin coupling dynamics (in a range of -40 cm-1 to -500 cm-1). e-aq···e-aq can recombine to e22-aq through a unique solvent fluctuation-controlled gradual-flowing mechanism, and enlarging fluctuation can promote the conversion. Interestingly, we directly observe that e22-aq as the precursor can trigger hydrogen evolution via unique continuous spontaneous double proton transfer to the dielectron with a short-lived H-aq intermediate, but e-aq···e-aq does not directly. This is the first direct observation for the connection between e22-aq and spontaneous hydrogen evolution including participation of H-aq in aqueous solution, bridging relevant experimental phenomena. This work also evidences an unnoticed process, the double proton transfer mediated charge separation, and presents the first detailed analysis regarding the evolution dynamics of e22-aq for the understanding of the radiolysis reactions in aqueous solutions.

Solvent polarity dependent excited state hydrogen bond effects and intramolecular double proton transfer mechanism for 2-hydroxyphenyl-substituted benzo[1,2-d:4,5-d’]bisimidazole system

In this work, we probe into the photo-induced excited state hydrogen bonding interactions and excited state proton transfer (ESPT) behaviors for a representative benzo[1,2-d:4,5-d’]bisimidazole derivative (i.e., 2-hydroxyphenyl-substituted benzo[1,2-d:4,5-d’]bisimidazole (HPBB)) compound. In view of aprotic solvents with different polarities, cyclohexane (CYH), dichloromethane (DCM) and acetonitrile (MeCN) solvents are considered. Analyzing hydrogen-bond geometrical parameters, infrared (IR) vibrational spectra, Mayer bond order and predicting hydrogen bonding energy (E(HB)), we verify dual hydrogen bonds of HPBB are strengthened in S1 state. Particularly, in nonpolar solvent, the enhanced excited state hydrogen bonds become more obvious. The intriguing charge redistribution and frontier molecular orbitals (MOs) reveal hydrogen bonding acceptance ability of acceptor moieties becomes stronger, which plays a crucial role in capturing hydroxyl proton via photoexcitation. To check and explore ESIPT mechanism, we present the solvent polarity dependent asynchronous excited state intramolecular double proton transfer (ESIDPT) mechanism. That is, nonpolar solvent promotes excited state intramolecular single proton transfer (ESISPT) process for HPBB, while polar solvent contributes to ESIDPT behavior with the primary single proton-transfer product in S1 state. This work not only makes a rational attribution to experimental phenomena, but also clarifies detailed excited state behaviors for HPBB and presents regulating ESIPT mechanism via solvent polarity.

Phototautomerism of Alloxazine in Acetic acid – Water solvent systems

The photophysics of Alloxazine was studied in Acetic acid – Water solvent systems which included neutral water (pH = 7), pure acetic acid, and their binary mixtures. Alloxazine was found to exhibit tautomerization into Isoalloxazine over a time-scale which depended on the nature of the solvent. While the process was too fast in neutral water to be detected with a ~100 ps time-resolution, it was drastically inhibited on addition of small quantities of acetic acid, displaying a remarkably long time-constant ~700 ps. However, further addition of acetic acid gradually decreased the time-constant, until it finally reached ~280 ps in pure acetic acid. Quantum chemical calculations indicated that the tautomerization occurred via Excited-state Double Proton Transfer (ESDPT) mechanism in cyclic intermolecular H-bonded complexes of Alloxazine with the solvent molecule (water or acetic acid). This involved reorganization of the H-bonded structures in the S1 energy surface, causing effective transfer of the N(1) bound proton of Alloxazine to its N(10) position, producing the Isoalloxazine tautomer. The H-bond reorganization of the complexes were strongly coupled with the solvation dynamics of the solvent concerned, and this helped to explain the large divergence of the tautomerization time-constants in the different solvents and solvent mixtures used in this study.

High-temperature, solvent-induced proton transfer and double proton transfer in adenine–thymine replaced with deazaadenine

One way to improve DNA conductivity is to change the mobility of carriers via functional group modification. Based on molecular dynamics calculations, this paper discusses proton transfer between bases after replacing the nitrogen atoms at the 3 and 7 positions in adenine by carbon and hydrogen. At a high temperature, charge localization is improved, with the charge located on a single base. Additionally, proton transfer and double proton transfer appear at a high temperature. The effects of the aqueous solution, temperature, and functional group on proton transfer are analyzed and discussed. The improved charge localization and reduction in the effect of temperature in the substituted adenine provide great potential for improving charge transport in adenine–thymine base pairs.

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP.

Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2′-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1′-β-D-2′- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.

The influence of base pair tautomerism on single point mutations in aqueous DNA.

The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.

Photoinduced double proton transfer in the glyoxal-methanol complex along T1 reaction path – a quantum chemical topological study

The experimentally confirmed double proton transfer (DPT) reaction in glyoxal-methanol complex follows a complicated mechanism triggered by the excitation of the complex to the lowest singlet excited electronic state. The mechanism involves two complementary pathways, the first of which proceeds exclusively in the singlet manifold. The competing one, which is studied here with the use of quantum chemical topological methods, involves the lowest triplet state. Both Atoms-in-Molecules approach and Electron Localizability Indicator based approach demonstrate that protons dressed with some amount of electron density migrate to and from the methanol, which leads to the rearrangement of four covalent bonds. The transition structure nearly coincides with the dissociation of the covalent CH bond in glyoxal. DPT proceeds through a structure formed by the protonated [MeOH2]+0.66, with H atoms equidistant to O atom, and deprotonated [C2O2H]−0.66. The key stages of the evolution of the crucial covalent bonds along the intrinsic reaction path have been demonstrated.

DUAL EMISSION OF 2-AMINO-4-METHYLPYRIMIDINE: A THEORETICAL STUDY

DFT and TD-DFT calculations at the B3LYP/LANL2DZ level of theory are performed in order to explain the origins of dual fluorescence and uncover the relaxation pathways of 2-amino-4-methylpyrimidine (L). The computations are in good agreement with experimental data. A high-energy emission band in the photoluminescence spectrum of 2-amino-4-methylpyrimidine (λmax = 350 nm) is related to the fluorescence of monomer L. Comparison of calculated and experimental IR and absorption spectra reveals that in the solid state L molecules form supramolecular {N–H···N}n hydrogen bonded associates. The formation of such associates favors the excited state double proton transfer (ESDPT). Calculated 2D potential energy curves for the ground and first singlet excited states of dimeric associates L2 indicate the presence of two stable forms, L2-amino and L2-imino. The low-energy band in the emission spectrum of 2-amino-4-methylpyrimidine (λmax = 445 nm) is probably associated with the fluorescence of the L2-imino form. Both fluorescence bands have a mixed π–π*, n–π* character as is evidenced by frontier orbitals involved in S1–S0 transitions.

Nonequilibrium Dynamics of Proton-Coupled Electron Transfer in Proton Wires: Concerted but Asynchronous Mechanisms.

The coupling between electrons and protons and the long-range transport of protons play important roles throughout biology. Biomimetic systems derived from benzimidazole-phenol (BIP) constructs have been designed to undergo proton-coupled electron transfer (PCET) upon electrochemical or photochemical oxidation. Moreover, these systems can transport protons along hydrogen-bonded networks or proton wires through multiproton PCET. Herein, the nonequilibrium dynamics of both single and double proton transfer in BIP molecules initiated by oxidation are investigated with first-principles molecular dynamics simulations. Although these processes are concerted in that no thermodynamically stable intermediate is observed, the simulations predict that they are predominantly asynchronous on the ultrafast time scale. For both systems, the first proton transfer typically occurs ∼100 fs after electron transfer. For the double proton transfer system, typically the second proton transfer occurs hundreds of femtoseconds after the initial proton transfer. A machine learning algorithm was used to identify the key molecular vibrational modes essential for proton transfer: a slow, in-plane bending mode that dominates the overall inner-sphere reorganization, the proton donor–acceptor motion that leads to vibrational coherence, and the faster donor–hydrogen stretching mode. The asynchronous double proton transfer mechanism can be understood in terms of a significant mode corresponding to the two anticorrelated proton donor–acceptor motions, typically decreasing only one donor–acceptor distance at a time. Although these PCET processes appear concerted on the time scale of typical electrochemical experiments, attaching these BIP constructs to photosensitizers may enable the detection of the asynchronicity of the electron and multiple proton transfers with ultrafast two-dimensional spectroscopy. Understanding the fundamental PCET mechanisms at this level will guide the design of PCET systems for catalysis and energy conversion processes.

A theoretical study on water-assisted excited state double proton transfer process in substituted 2,7-diazaindole-H2O complex

The substituted effect on the first excited-state proton transfer (ESPT) process in 2,7-diazaindole-H2O (2,7-DAI-H2O) complex in water was studied in detail at the TD-M06-2X/6–311 + G(d, p) level. The frontier molecular orbital, geometries, reaction mechanism and energies of ESPT process with different substituent have been analyzed. ESPT process in the title complex occurred concertedly but highly asynchronously no matter of the electronic nature of substituent. The absorption and fluorescence peaks, H-bond distances, asynchronicity of ESPT and barrier height were affected by the substituent. The Hammett’s substituent constant had linear correlation with the difference between the sum of N1−O11 and O11−N7 distances in the reactant and that in the TS and Mulliken charge of H3O+.

Density functional theory studies on cytosine analogues for inducing double-proton transfer with guanine

To induce double-proton transfer (DPT) with guanine in a biological environment, 12 cytosine analogues (Ca) were formed by atomic substitution. The DPT reactions in the Watson–Crick cytosine–guanine model complex (Ca0G) and 12 modified cytosine–guanine complexes (Ca1-12G) were investigated using density functional theory methods at the M06-2X/def2svp level. The intramolecular proton transfers within the analogues are not facile due to high energy barriers. The hydrogen bond lengths of the Ca1-12G complexes are shorter than those in the Ca0G complex, which are conducive to DPT reactions. The DPT energy barriers of Ca1-12G complexes are also lower than that of the Ca0G complex, in particular, the barriers in the Ca7G and Ca11G complexes were reduced to −1.33 and −2.02 kcal/mol, respectively, indicating they are significantly more prone to DPT reactions. The DPT equilibrium constants of Ca1-12G complexes range from 1.60 × 100 to 1.28 × 107, among which the equilibrium constants of Ca7G and Ca11G are over 1.0 × 105, so their DPT reactions may be adequate. The results demonstrate that those cytosine analogues, especially Ca7 and Ca11, are capable of inducing DPT with guanine, and then the guanine tautomer will form mismatches with thymine during DNA replication, which may provide new strategies for gene therapy.

How the atomic electron-accepting ability affect the double ESIPT process of 2,5-bis(benzoxazol-2-yl)thiophene-3,4-diol?

By adopting the density functional theory (DFT) and time-dependent DFT (TD-DFT) methods, the effects of atomic electron-accepting ability on the double excited state intramolecular proton transfer (ESIPT) processes of the molecules (BBO, BBT and BBSe) were systematically investigated. The obtained bond lengths, bond angles and IR vibration analysis prove that the strength of the hydrogen bonds in the three molecules gradually increases from BBO to BBT and BBSe. Moreover, the potential energy surfaces and topology analysis indicate that all the three molecules prefer to the ultrafast stepwise double ESIPT reaction in the S1 state. And the excited state proton transfer occurs more easily in the studied molecular systems along with the weakened electron-accepting ability of atom. It is concluded that the decreasing electron-accepting ability of atom can promote the molecular ESIPT behavior, which provides the theoretical basis for the synthesis of the new molecular systems with double ESIPT properties.

Photoinduced Double Proton Transfer in the Glyoxal-Methanol Complex Revisited: The Role of the Excited States.

Under irradiation in the visible range, the glyoxal-methanol complex in a cryogenic argon matrix undergoes a double proton transfer (DPT) reaction through which the glyoxal molecule isomerizes into hydroxyketene. In this work, we employ electronic structure simulations in order to shed more light on the underlying mechanism. Rewardingly, we find that the lowest singlet excited state (S1) of the complex acts as a gateway to two previously unknown isomerization pathways, of which one takes place entirely in the singlet manifold and the other also involves the lowest triplet state (T1). Both of these pathways are fully compatible with the available experimental data, implying that either or both are operative under experimental conditions. In either pathway, the methanol molecule acts as a proton shuttle between the proton-donating and proton-accepting sites of glyoxal, resulting in a dramatic lowering of the potential energy barrier to isomerization with respect to the case of isolated glyoxal. The occurrence of DPT in the singlet manifold is demonstrated directly with the use of nonadiabatic molecular dynamics simulations at the spin-flip time-dependent density functional theory level.

Proton Transfer vs Complex Formation Channels in Ionized Formic Acid Dimer: A Direct Ab Initio Molecular Dynamics Study

Photoirradiation to a hydrogen-bonded system plays an important role in the initial DNA and enzyme damage processes. The formic acid (FA) dimer is a model compound of double proton transfer systems, such as DNA base pairs. In the present study, the reactions of the FA dimer cation, formed upon ionization of the neutral dimer, have been investigated by the direct ab initio molecular dynamics method. Two reaction channels were identified for the FA dimer cation: complex formation and proton transfer (PT). In the complex formation channel, the carbonyl oxygen atoms of the two FA monomers were bound symmetrically, and a face-to-face complex was formed. In the PT channel, the proton of FA+ was transferred to FA, forming the H+(HCOOH)--HCO2 radical cation as product. At low temperature, the complex channel was dominant, whereas the PT channel increased with increasing temperature. The asymmetric spin distribution on the FA dimer cation exhibited a strong correlation with the PT channel.

Mechanisms of the T-A to C-G transition studied by SMD simulations: Deamination vs tautomerisation

Abstract The T-A to C-G transition was obtained in gas and aqueous phases by applying steered molecular dynamic (SMD) simulations. Two different pathways were considered to explain the mechanism of the transition, which included water-molecule-assisted adenine deamination and tautomerisation of the T*-A* mispair via double proton transfer. In both pathways, the associations between nitrogenous bases of DNA, such as T-A, C-G, G-T* and C-A*, were also considered. In the gas phase, the transition via deamination was determined to be the most favourable (ΔG = 3.92 kcal·mol−1) while in solution tautomerisation was favoured (ΔG = 11.33 kcal·mol−1). The presence of solvent made the mutation more endergonic, slowed the reaction and increased its overall energy requirement and energy barrier. The lifetimes of T*-A* and C-G species formed in the tautomerisation pathway were very short, and C-G pair was only predicted to be capable of encoding the genetic sequence only when the transition followed the deamination path (τgas = 1.64·10+36 s, τsolution = 1.81·10+25 s). Molecular structures involved in these mechanisms were analysed along the reaction path, which allowed us to visualise the energy profiles of the reactions over time and calculate their kinetic and thermodynamic properties.

Spectral Decomposition of the Reaction Force Constant.

Qualitative relationships between the reaction force constant κ(ξ), the second derivative of the potential energy V(ξ), and the reactive vibrational mode that drives the reaction in the transition state region have been used in the past to measure the synchronicity of key chemical events that lead a chemical reaction. In this work, we provide a formal demonstration that κ(ξ) can be expressed in terms of the frequencies of normal modes at each point of the reaction path. This produce a decomposition of κ(ξ) that is used to analyze few representatives chemical reactions, a series of intramolecular proton transfer on formic, thioformic and dithioformic acids, and an intermolecular double proton transfer in the HNS2:H2O complex. It has been found that this partitioning allows to identify unambigously the reactive mode that drives the reaction at each point along the reaction coordinate thus giving relevant and detailed information about the mechanism of the chemical reactions under study.