Refreshing the Legacy of Rudolf Nietzki: Benzene-1,2,4,5-tetramine and Related Compounds.

Like hydroquinones and quinones, aromatic compounds with multiple NH2 groups and the corresponding quinonediimines have the potential to serve as components of useful redox-active organic materials. Benzene-1,2,4,5-tetramine (BTA) and its oxidized form BTA-H2 offer a promising redox pair of this type, and the compounds have proven to be useful in many areas of chemistry. However, key aspects of their behavior have remained poorly studied, such as the nature of their protonated forms, their preferred molecular structures, their reactivity, and their organization in condensed phases. In the present work, we have used a combination of improved methods of synthesis, computation, spectroscopic studies, and structural analyses to develop a deeper understanding of BTA, BTA-H2, their salts, and related compounds. The new knowledge is expected to accelerate exploitation of the compounds in areas of materials science where desirable properties can only be attained by properly controlling the organization of molecular components.

Diphenoquinhydrones and Related Hydrogen-Bonded Charge-Transfer Complexes.

Benzoquinone and hydroquinone cocrystallize to form quinhydrone, a 1:1 complex with a characteristic structure in which the components are positioned by hydrogen bonds and charge-transfer interactions. We have found that analogous diphenoquinhydrones can be made by combining 4,4'-diphenoquinones with the corresponding 4,4'-dihydroxybiphenyls. In addition, mixed diphenoquinhydrones can be assembled from components with different substituents, and mismatched quinhydrones can be made from benzoquinones and dihydroxybiphenyls. In all cases, the components of the resulting structures are linked in alternation by O-H···O hydrogen bonds to form essentially planar chains, which stack to produce layers in which π-donors and π-acceptors are aligned by charge-transfer interactions. Geometric parameters, computational studies, and spectroscopic properties of diphenoquinhydrones show that the key intermolecular interactions are stronger than those in simple quinhydrone analogues. These findings demonstrate that the principles of modular construction underlying the formation of classical quinhydrones can be generalized to produce a broad range of hydrogen-bonded charge-transfer materials in which the components are positioned by design.

Diphenoquinones Redux.

Benzoquinones can undergo reversible reductions and are attractive candidates for use as active materials in green carbon-based batteries. Related compounds of potential utility include 4,4'-diphenoquinones, which have extended quinonoid structures with two carbonyl groups in different rings. Diphenoquinones are a poorly explored class of compounds, but a wide variety can be synthesized, isolated, crystallized, and fully characterized. Experimental and computational approaches have established that typical 4,4'-diphenoquinones have nearly planar cores in which two cyclohexadienone rings are joined by an unusually long interannular C═C bond. Derivatives unsubstituted at the 3,3',5,5'-positions react readily by hydration, dimerization, and other processes. Association of diphenoquinones in the solid state normally produces chains or sheets held together by multiple C-H···O interactions, giving structures that differ markedly from those of the corresponding 4,4'-dihydroxybiphenyls. Electrochemical studies in solution and in the solid state show that diphenoquinones are reduced rapidly and reversibly at potentials higher than those of analogous benzoquinones. Together, these results help bring diphenoquinones into the mainstream of modern chemistry and provide a foundation for developing redox-active derivatives for use in carbon-based electrochemical devices.

Computational Insight into Cu-Catalyzed Csp-S Coupling to Form a Macrocyclic Alkynyl Sulfide.

Copper-catalyzed Csp-S cross-coupling is known to form rare macrocyclic alkynyl sulfides. Computational studies now suggest a mechanism for the reaction pathway. Upon formation of Cu-S species, subsequent α-addition/elimination at the ethynylic carbon affords the desired macrocycle.

Predicting pKa Values of Quinols and Related Aromatic Compounds with Multiple OH Groups.

Quinonoid compounds play central roles as redox-active agents in photosynthesis and respiration and are also promising replacements for inorganic materials currently used in batteries. To design new quinonoid compounds and predict their state of protonation and redox behavior under various conditions, their pKa values must be known. Methods that can predict the pKa values of simple phenols cannot reliably handle complex analogues in which multiple OH groups are present and may form intramolecular hydrogen bonds. We have therefore developed a straightforward method based on a linear relationship between experimental pKa values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pKa values when intramolecular hydrogen bonds are present. Our approach has been validated by showing that predicted and experimental values for over 100 quinols and related compounds differ by an average of only 0.3 units. This accuracy makes it possible to select proper pKa values when experimental data vary, predict the acidity of quinols and related compounds before they are made, and determine the sites and orders of deprotonation in complex structures with multiple OH groups.

Electrochemically Triggered Dynamics within a Hybrid Metal-Organic Electrocatalyst.

A wide array of systems, ranging from enzymes to synthetic catalysts, exert adaptive motifs to maximize their functionality. In a related manner, select metal-organic frameworks (MOFs) and similar systems exhibit structural modulations under stimuli such as the infiltration of guest species. Probing their responsive behavior in situ is a challenging but important step toward understanding their function and subsequently building functional systems. In this report, we investigate the dynamic behavior of an electrocatalytic Mn-porphyrin-containing MOF system (Mn-MOF). We discover, using a combination of electrochemistry and in situ probes of UV-vis absorption, resonance Raman, and infrared spectroscopy, a restructuration of this system via a reversible cleavage of the porphyrin carboxylate ligands under an applied voltage. We further show, by combining experimental data and DFT calculations, as a proof of concept, the capacity to utilize the Mn-MOF for electrochemical CO2 fixation and to spectroscopically capture the reaction intermediates in its catalytic cycle. The findings of this work and the methodology developed open opportunities in the application of MOFs as dynamic, enzyme-inspired electrocatalytic systems.

Moderately strong phenols dissociate by forming an ion-pair kinetic intermediate.

We show computational evidence that ground-state moderately strong hydroxyarenes (Ar-OH, pKa ∼ 0) dissociate by forming an ion-pair intermediate that lives for 3-5 ps. The concentration of this intermediate is approximately 2 times smaller than that of the un-ionized acid at pH ∼ 0.6 and is characterized by average C-O bond lengths (1.30 Å) that are intermediate between those of un-ionized (1.29 Å) and fully dissociated (1.34 Å) species. During the lifetime of the ion-pair intermediate the excess proton fluctuates between the oxygen atom of the phenolic moiety and those of water molecules in the first and second solvation shells on a subpicosecond time scale (∼100-300 fs).

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation.

We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa∼0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ∼50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ∼1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 Šcan take place on a sub-picosecond timescale.

Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions.

Recently, the vacuum-phase molecular polarizability tensor of various molecules has been accurately modeled (Truchon et al., J Chem Theory Comput 2008, 4, 1480) with an intramolecular continuum dielectric model. This preliminary study showed that electronic polarization can be accurately modeled when combined with appropriate dielectric constants and atomic radii. In this article, using the parameters developed to reproduce ab initio quantum mechanical (QM) molecular polarizability tensors, we extend the application of the "electronic polarization from internal continuu" (EPIC) approach to intermolecular interactions. We first derive a dielectric-adapted least-square-fit procedure similar to RESP, called DRESP, to generate atomic partial charges based on a fit to a QM abinitio electrostatic potential (ESP). We also outline a procedure to adapt any existing charge model to EPIC. The ability of this to reproduce local polarization, as opposed to uniform polarization, is also examined leading to an induced ESP relative root mean square deviation of 1%, relative to ab initio, when averaged over 37 molecules including aromatics and alkanes. The advantage of using a continuum model as opposed to an atom-centered polarizable potential is illustrated with a symmetrically perturbed atom and benzene. We apply EPIC to a cation-pi binding system formed by an atomic cation and benzene and show that the EPIC approach can accurately account for the induction energy. Finally, this article shows that the ab initio electrostatic component in the difficult case of the H-bonded 4-pyridone dimer, a highly polar and polarized interaction, is well reproduced without adjusting the vacuum-phase parameters.

Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: first-principles free energy and entropy calculations.

We introduce a novel approach to compute dissociation free energy and entropy values in simulations that employ a density functional theory description of the acidic moiety and of the solvent. The approach consists of utilizing an alchemical transformation of a weak acid A-COOH into the strong acid B-COOH, which makes it practical to employ alchemical free energy perturbation methods in the context of ab initio molecular dynamics simulations. The present alchemical transformation circumvents the need to tackle changes in the total number of electrons and atoms by replacing the chemical residue responsible for the change in acidity with an easily tunable external effective potential. Our investigation demonstrates that (1) a simple but effective class of external potentials that control acidity changes in the acetic/trifluoroacetic acid series can be achieved by replacing the methyl and trifluoromethyl substituents by screened dipoles. Using this dipole-field/quantum-mechanics (DF/QM) approach one can predict gas-phase geometries, proton dissociation energies, total dipole moments, and water binding energies in good agreement with full-QM values. (2) The resulting alchemical perturbation calculations are stable and well converged and allow one to compute absolute pK(a) values whose accuracy is limited primarily by the exchange-correlation functional employed: H-COOH=2.5+/-0.6 (full-QM calculation), 3.7 (exp); F(3)C-COOH=0.4+/-0.6 (DF/QM calculation), 0.5 (exp); H(3)C-COOH=3.1+/-0.7 (DF/QM calculation), 4.7 (exp); 3) Our DF/QM model predicts that the difference in acidity between H-COOH and H(3)C-COOH is dominated by solvent entropy effects, in excellent agreement with experimental observations. The calculated difference between the dissociation energies of these acids is DeltaDelta(d)U=0.0+/-0.26 kcal/mol while the experimental value is 0.0+/-0.1 kcal/mol.

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model.

Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Bronsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa congruent with 1) as a model for excited-state HPTS( *) (pKa congruent with 1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

Toward understanding the dissociation of weak acids in water: 1. Using ir spectroscopy to identify proton-shared hydrogen-bonded ion-pair intermediates.

Cryogenic conditions favor the formation of ion-pair dissociation intermediates in amorphous mixtures of HF and H(2)O, making possible their characterization by means of infrared spectroscopy. The experimental infrared spectra show a structurally rich "continuous" absorption ranging from 1000 to 3400 cm(-1), which, in principle, contains important information regarding the microscopic structure of the aforementioned dissociation intermediates. Herein, we demonstrate that this microscopic information can be extracted by comparing and contrasting experimental spectra with those obtained by means of carefully designed first-principles molecular dynamics calculations. Very good, systematic agreement between theoretical and experimental spectra can be obtained for HF/H(2)O mixtures of various compositions, revealing the presence of proton-shared, dissociation intermediates F(delta-) * * * H * * * (delta+)OH(2). The existence of similar proton-shared, hydrogen-bonded intermediates of ionization, that are stable in solution, but not in the gas phase, has been previously suggested by other groups, using, among other techniques, low temperature NMR data and aprotic, dipolar, solvents. Our investigation reveals that similar structures are also stable in aqueous solutions of HF. We discuss some of the implications of the present findings as far as the mechanism of dissociation of weak acids is concerned.

Molecular polarizabilities in aqueous proton transfer reactions.

Dipole polarizabilities of individual ions and molecules are computed from first principles in three condensed-phase systems: pure water, pure hydrofluoric acid, and an equimolar mixture of water and hydrofluoric acid in which HF is mostly ionized. We find that the polarizability of fluorine and oxygen centers varies linearly with the value of the bond order, which measures the local degree of advancement of the ionization reaction F-H+H(2)O<==>[F(delta-).H.(delta+)OH(2)]<==>F(-)+H(3)O(+). This observation explains the validity of the Lorentz-Lorenz formula for mixtures of acids and water and could have important practical consequences concerning the construction of empirical polarizable reactive force fields. Our results are consistent with the Mulliken charge-transfer picture of proton transfer reactions. The present results also suggest that the average isotropic polarizability of a chemical entity changes substantially only when that entity is involved in charge-transfer processes.

Spectral signatures and molecular origin of acid dissociation intermediates.

The existence of a broad, mid-infrared absorption ranging from 1000 to 3000 cm(-1) is usually interpreted as a signature for the existence of protonated water networks. Herein, we use cryogenic mixtures of water and hydrogen fluoride (HF) and show experimental and computational evidence that similarly wide absorptions can be generated by a broad distribution of proton-shared and ion pair complexes. In the present case, we demonstrate that the broadening is mainly inhomogeneous, reflecting the fact that the topology of the first solvation shell determines the local degree of ionization and the shared-proton asymmetric stretching frequency within H2O x HF complexes. The extreme sensitivity of the proton transfer potential energy hypersurface to local hydrogen bonding topologies modulates its vibrational frequency from 2800 down to approximately 1300 cm(-1), the latter value being characteristic of solvation geometries that yield similar condensed-phase proton affinities for H2O and fluoride. By linking the local degree of ionization to the solvation pattern, we are able to propose a mechanism of ionization for HF in aqueous solutions and to explain some of their unusual properties at large concentrations. However, an important conclusion of broad scientific interest is our prediction that spectral signatures that are normally attributed to protonated water networks could also reveal the presence of strong hydrogen bonds between un-ionized acids and water molecules, with important consequences to spectroscopic investigations of biologically relevant proton channels and pumps.

Ab initio and empirical model MD simulation studies of solvent effects on the properties of N-methylacetamide along a cis-trans isomerization pathway.

The properties of N-methylacetamide along a cis-trans isomerization pathway described by twisting about the C(O)-N bond are examined at finite temperature both in vacuo and in explicit water solvent. Two distinctly different theoretical descriptions, an ab initio (DFT-BLYP) and an empirical (CHARMM22) model, are studied in order to permit an assessment of the dominant forces active in the system. An analysis of the solvent structure at equilibrium and changes in solvation structure accompanying isomerization is, therefore, given for each model. Many-body polarization effects absent under CHARMM22 but present in the ab initio model are found to have a profound influence on the system. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is examined in order to shed further light on changes in peptide "partial-double" bond character [C(O)-N] as isomerization takes place. A new statistical-mechanical interpretation of the entropy change during a chemical reaction is presented to help interpret the thermochemistry of the simple reaction.

Donor-Bridge-Acceptor Proton Transfer in Aqueous Solution.

We use ab initio molecular dynamics to study proton transfer in a donor-bridge-acceptor system in which the bridge is a single water molecule and the entire system is embedded in aqueous solution. The results, based on a large number of proton transfer trajectories, demonstrate that the dominant charge-transfer pathway is a subpicosecond "through bridge" event in which the bridge adopts an Eigen-like (hydronium) structure. We also identify another state in which the bridge forms a Zundel-like configuration with the acceptor that appears to be a dead end for the charge transfer. The reaction coordinate is inherently multidimensional and, as we demonstrate, cannot be given in terms of either local structural parameters of the donor-bridge-acceptor system or local solvent coordination numbers.

Concerted and Sequential Proton Transfer Mechanisms in Water-Separated Acid-Base Encounter Pairs.

The proton transfer mechanisms involved inside aqueous, solvent-separated encounter complexes between phenol and carboxyl moieties are studied using ab initio molecular dynamics and computational time-resolved vibrational spectroscopy. This model framework can be viewed as a ground-state analog of the excited-state proton transfer reactions that have been actively investigated using ultrafast spectroscopy. Three qualitatively distinct proton transfer pathways are observed in the simulations. These can be described as direct concerted, direct sequential, and through bulk transfers. The primary difference between the sequential and concerted mechanism is the involvement of a reaction intermediate in which the proton fluctuates for several picoseconds through the hydrogen bonds connecting donor and acceptor but resides primarily on an intervening water molecule in the encounter complex. These results contribute to our molecular level understanding of the diverse processes involved in proton transfer within water-separated encounter complexes.

On the formation of proton-shared and contact ion pair forms during the dissociation of moderately strong acids: an Ab initio molecular dynamics investigation.

Acid ionization and dissociation are phenomena that play a fundamental role in chemistry and biology, but their microscopic details are largely unknown. We use ab initio molecular dynamics to identify and characterize various structures that are formed along the pathway of dissociation of trifluoroacetic acid (pK(a) = 0.5). The present results demonstrate that solutions of moderately strong (-1

Accurate Molecular Polarizabilities Based on Continuum Electrostatics.

A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter.