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

Accelerated simulation method for charge regulation effects

The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon, charge regulation (CR), in theoretical and computational models requires dynamic, configuration-dependent recalculation of surface charges and is therefore typically approximated by assuming constant net charge on particles. Various computational methods exist that address this. We present an alternative, particularly efficient CR Monte Carlo method (CR-MC), which explicitly models the redistribution of individual charges and accurately samples the correct grand-canonical charge distribution. In addition, we provide an open-source implementation in the large-scale Atomic/Molecular Massively Parallel Simulator molecular dynamics (MD) simulation package, resulting in a hybrid MD/CR-MC simulation method. This implementation is designed to handle a wide range of implicit-solvent systems that model discreet ionizable groups or surface sites. The computational cost of the method scales linearly with the number of ionizable groups, thereby allowing accurate simulations of systems containing thousands of individual ionizable sites. By matter of illustration, we use the CR-MC method to quantify the effects of CR on the nature of the polyelectrolyte coil-globule transition and on the effective interaction between oppositely charged nanoparticles.

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.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

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).

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.

Disproportionation of bromous acid HOBrO by direct O-transfer and via anhydrides O(BrO)2 and BrO-BrO2. An ab initio study of the mechanism of a key step of the Belousov-Zhabotinsky oscillating reaction

The results are reported of an ab initio study of the thermochemistry and of the kinetics of the HOBrO disproportionation reaction 2HOBrO (2) ⇄ HOBr (1) + HBrO(3) (3), reaction ( R4' ), in gas phase (MP2(full)/6-311G*) and aqueous solution (SMD(MP2(full)/6-311G*)). The reaction energy of bromous acid disproportionation is discussed in the context of the coupled reaction system R2-R4 of the FKN mechanism of the Belousov-Zhabotinsky reaction and considering the acidities of HBr and HOBrO(2). The structures were determined of ten dimeric aggregates 4 of bromous acid, (HOBrO)(2), of eight mixed aggregates 5 formed between the products of disproportionation, (HOBr)(HOBrO(2)), and of four transition states structures 6 for disproportionation by direct O-transfer. It was found that the condensation of two HOBrO molecules provides facile access to bromous acid anhydride 7, O(BrO)(2). A discussion of the potential energy surface of Br(2)O(3) shows that O(BrO)(2) is prone to isomerization to the mixed anhydride 8, BrO-BrO(2), and to dissociation to 9, BrO, and 10, BrO(2), and their radical pair 11. Hence, three possible paths from O(BrO)(2) to the products of disproportionation, HOBr and HOBrO(2), are discussed: (1) hydrolysis of O(BrO)(2) along a path that differs from its formation, (2) isomerization of O(BrO)(2) to BrO-BrO(2) followed by hydrolysis, and (3) O(BrO)(2) dissociation to BrO and BrO(2) and their reactions with water. The results of the potential energy surface analysis show that the rate-limiting step in the disproportionation of HOBrO consists of the formation of the hydrate 12a of bromous acid anhydride 7 via transition state structure 14a. The computed activation free enthalpy ΔG(act)(SMD) = 13.6 kcal/mol for the process 2·2a → [14a](‡) → 12a corresponds to the reaction rate constant k(4) = 667.5 M(-1) s(-1) and is in very good agreement with experimental measurements. The potential energy surface analysis further shows that anhydride 7 is kinetically and thermodynamically unstable with regard to hydrolysis to HOBr and HOBrO(2) via transition state structure 14b. The transition state structure 14b is much more stable than 14a, and, hence, the formation of the "symmetrical anhydride" from bromous acid becomes an irreversible reaction for all practical purposes because 7 will instead be hydrolyzed as a "mixed anhydride" to afford HOBr and HOBrO(2). The mixed anhydride 8, BrO-BrO(2), does not play a significant role in bromous acid disproportionation.

Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation

Absolute pKa values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [ Cheng , J. ; Sulpizi , M. ; Sprik , M. J. Chem. Phys. 2009 , 131 , 154504 ]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed solvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pKa units with a maximum error of 4.0 pKa units. The estimated mean statistical uncertainty due to the finite length of the trajectories is ±1.1 pKa units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments.

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.