Calculation of the absolute hydration enthalpy and free energy of H+ and OH−

Simulating Metal-Imidazole Complexes

One commonly observed binding motif in metalloproteins involves the interaction between a metal ion and histidine's imidazole side chains. Although previous imidazole-M(II) parameters established the flexibility and reliability of the 12-6-4 Lennard-Jones (LJ)-type nonbonded model by simply tuning the ligating atom's polarizability, they have not been applied to multiple-imidazole complexes. To fill this gap, we systematically simulate multiple-imidazole complexes (ranging from one to six) for five metal ions (Co(II), Cu(II), Mn(II), Ni(II), and Zn(II)) which commonly appear in metalloproteins. Using extensive (40 ns per PMF window) sampling to assemble free energy association profiles (using OPC water and standard HID imidazole charge models from AMBER) and comparing the equilibrium distances to DFT calculations, a new set of parameters was developed to focus on energetic and geometric features of multiple-imidazole complexes. The obtained free energy profiles agree with the experimental binding free energy and DFT calculated distances. To validate our model, we show that we can close the thermodynamic cycle for metal-imidazole complexes with up to six imidazole molecules in the first solvation shell. Given the success in closing the thermodynamic cycles, we then used the same extended sampling method for six other metal ions (Ag(I), Ca(II), Cd(II), Cu(I), Fe(II), and Mg(II)) to obtain new parameters. Since these new parameters can reproduce the one-imidazole geometry and energy accurately, we hypothesize that they will reasonably predict the binding free energy of higher-level coordination numbers. Hence, we did not extend the analysis of these ions up to six imidazole complexes. Overall, the results shed light on metal-protein interactions by emphasizing the importance of ligand-ligand interaction and metal-π-stacking within metalloproteins.

The role of charge in microdroplet redox chemistry

In charged water microdroplets, which occur in nature or in the lab upon ultrasonication or in electrospray processes, the thermodynamics for reactive chemistry can be dramatically altered relative to the bulk phase. Here, we provide a theoretical basis for the observation of accelerated chemistry by simulating water droplets of increasing charge imbalance to create redox agents such as hydroxyl and hydrogen radicals and solvated electrons. We compute the hydration enthalpy of OH- and H+ that controls the electron transfer process, and the corresponding changes in vertical ionization energy and vertical electron affinity of the ions, to create OH• and H• reactive species. We find that at ~ 20 - 50% of the Rayleigh limit of droplet charge the hydration enthalpy of both OH- and H+ have decreased by >50 kcal/mol such that electron transfer becomes thermodynamically favorable, in correspondence with the more favorable vertical electron affinity of H+ and the lowered vertical ionization energy of OH-. We provide scaling arguments that show that the nanoscale calculations and conclusions extend to the experimental microdroplet length scale. The relevance of the droplet charge for chemical reactivity is illustrated for the formation of H2O2, and has clear implications for other redox reactions observed to occur with enhanced rates in microdroplets.

Solvation energies of the ferrous ion in water and in ammonia at various temperatures

CONTEXT

The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion.

METHOD

All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.

Experimental Compilation and Computation of Hydration Free Energies for Ionic Solutes

Although charged solutes are common in many chemical systems, traditional solvation models perform poorly in calculating solvation energies of ions. One major obstacle is the scarcity of experimental data for solvated ions. In this study, we release an experiment-based aqueous ionic solvation energy data set, IonSolv-Aq, that contains hydration free energies for 118 anions and 155 cations, more than 2 times larger than the set of hydration free energies for singly charged ions contained in the 2012 Minnesota Solvation Database commonly used in benchmarking studies. We discuss sources of systematic uncertainty in the data set and use the data to examine the accuracy of popular implicit solvation models COSMO-RS and SMD for predicting solvation free energies of singly charged ionic solutes in water. Our results indicate that most SMD and COSMO-RS modeling errors for ionic solutes are systematic and correctable with empirical parameters. We discuss two systematic offsets: one across all ions and one that depends on the functional group of the ionization site. After correcting for these offsets, solvation energies of singly charged ions are predicted using COSMO-RS to 3.1 kcal mol-1 MAE against a challenging test set and 1.7 kcal mol-1 MAE (about 3% relative error) with a filtered test set. The performance of SMD is similar, with MAE against those same test sets of 2.7 and 1.7 kcal mol-1. These results underscore the importance of compiling larger experimental data sets to improve solvation model parametrization and fairly assess performance.

Putting together the puzzle of ion transfer in single-digit carbon nanotubes: mean-field meets ab initio

Nature employs channel proteins to selectively pass water across cell membranes, which inspires the search for bio-mimetic analogues. Carbon nanotube porins (CNTPs) are intriguing mimics of water channels, yet ion transport in CNTPs still poses questions. As an alternative to continuum models, here we present a molecular mean-field model that transparently describes ion coupling, yet unlike continuum models, computes ab initio all required thermodynamic quantities for the KCl salt and H⁺ and OH^- ions present in water. Starting from water transfer, the model considers the transfer of free ions, along with ion-pair formation as a proxy of non-mean-field ion-ion interactions. High affinity to hydroxide, suggested by experiments, making it a dominant charge carrier in CNTPs, is revealed as an exceptionally favorable transfer of KOH pairs. Nevertheless, free ions, coexisting with less mobile ion-pairs, apparently control ion transport. The model well explains the observed effects of salt concentration and pH on conductivity, transport numbers, anion permeation and its activation energies, and current rectification. The proposed approach is extendable to other sub-nanochannels and helps design novel osmotic materials and devices.

Antioxidant activity of erlotinib and gefitinib: theoretical and experimental insights

Erlotinib and gefitinib are quinazoline derivatives with antineoplastic properties. Usually, intake of antineoplastic agents results in much a greater degree of oxidative stress, i.e. the production of free radicals, than induced by cancer itself. Hence, anticancerous drugs must also exhibit antioxidant activity but this has not been studied thus far. In this study, the antioxidant activity of erlotinib and gefitinib was examined by experimental and computational studies. It was found that erlotinib and gefitinib exhibit good 2,2-dipheny l-1-picrylhydrazyl (DPPH) radical and hydroxyl radical scavenging (HRS) activities. In DPPH assay, the IC₅₀ for erlotinib and gefitinib were 0.584 and 0.696 mM, respectively, while IC₅₀ for HRS assay were 0.843 and 1.03 mM for erlotinib and gefitinib, respectively. Structural characteristics such as frontier molecular orbitals (FMOs), molecular electrostatic potential maps (MESPs), and global descriptive parameters were calculated at DFT/B3LYP/6-311++G (d,p) on the optimized geometries of erlotinib and gefitinib. UV-visible spectroscopy revealed the possible electronic transitions between the FMOs and their associated excitation energies of both drugs and found that erlotinib has π to π* transitions while gefitinib has π to π* and σ to π* transitions. To elucidate the antioxidant activity of erlotinib and gefitinib, three mechanisms namely hydrogen atom transfer (HAT), single electron transfer proton transfer (SETPT), and sequential proton-loss electron-transfer (SPLET) were employed and articulated the results in arithmetic parameters like bond dissociation energy (BDE), proton affinity (PA), ionization potential (IP), electron transfer enthalpy (ETE), and proton dissociation enthalpy (PDE). Further, molecular docking studies have been carried out to have a better understanding of binding sites and modes of interaction with a well-known antioxidant target protein monoamine oxidase-B (MAO-B) employing docking scores and types of interactions. All the calculated parameters point out that though gefitinib and erlotinib were interchangeable, erlotinib requires a lesser amount of energy for proton transfer and electron transfer, moreover it scavenges radicals easily.

Modeling Differential Enthalpy of Absorption of CO2 with Piperazine as a Function of Temperature

Temperature-dependent correlations for equilibrium constants (ln K) and heat of absorption (ΔH_abs) of different reactions (i.e., deprotonation, double deprotonation, carbamate formation, protonated carbamate formation, dicarbamate formation) involved in the piperazine (PZ)/CO₂/H₂O system have been calculated using computational chemistry based ln K values input to the Gibbs-Helmholtz equation. This work also presents an extensive study of gaseous phase free energy and enthalpy for different reactions using composite (G3MP2B3, G3MP2, CBS-QB3, and G4MP2) and density functional theory [B3LYP/6-311++G(d,p)] methods. The explicit solvation shell (ESS) model and SM8T solvation free energy coupled with gaseous phase density functional theory calculations give temperature-dependent reaction equilibrium constants for different reactions. Calculated individual and overall reaction equilibrium constants and enthalpies of different reactions involved in CO₂ absorption in piperazine solution are compared against experimental data, where available, in the temperature range 273.15-373 K. Postcombustion CO₂ capture (PCC) is a temperature swing absorption-desorption process. The enthalpy of the solution directly correlates with the steam requirement of the amine regeneration step. Temperature-dependent correlations for ln K and ΔH_abs calculated using computational chemistry tools can help evaluate potential PCC solvents' thermodynamics and cost-efficiency. These correlations can also be employed in thermodynamic models (e.g., e-UNIQUAC, e-NRTL) to better understand postcombustion CO₂ capture solvent chemistry.

Theoretical Insights into the Radical Scavenging Activity of Glipizide: DFT and Molecular Docking Studies

Glipizide is a N-sulfonylurea compound used in the treatment of hyperglycemia in patients with Type 2 diabetes mellitus. In the present study, DFT-based computational methods and molecular docking studies have been performed to systematically evaluate the radical scavenger behavior of the title molecule. Structural characteristics such as molecular descriptors, frontier molecular orbitals, molecular potential mapping, and Mulliken charge population have been investigated. Thermodynamic parameters like proton affinity (PA), ionization potential (IP), bond dissociation energy (BDE), electron transfer enthalpy (ETE), and proton dissociation enthalpy (PDE) related to three antiradical mechanisms namely hydrogen atom transfer (HAT), sequential electron transfer proton transfer (SETPT) and sequential proton loss electron transfer (SPLET) have been studied. Also, molecular docking studies have been carried out to have a theoretical understanding of the molecular mechanism and for the elucidation of binding mode/modes of a compound targeted through non-covalent interactions. The obtained results are of great significance in better understanding the reaction mechanism of the title molecule and open new perspectives for the design of new potent antioxidant agents.

Adsorption of small organic acids and polyphenols on hematite surfaces: Density Functional Theory + thermodynamics analysis

HYPOTHESIS

The interactions of organic molecules with mineral surfaces are influenced by several factors such as adsorbate speciation, surface atomic and electronic structure, and environmental conditions. When coupled with thermodynamic techniques, energetics from atomistic modeling can provide a molecular-level picture of which factors determine reactivity. This is paramount for evaluating the chemical processes which control the fate of these species in the environment.

EXPERIMENTS

Inner-sphere adsorption of oxalate and pyrocatechol on (001), (110), and (012) α-Fe₂O₃ surfaces was modeled using Density Functional Theory (DFT). Unique bidentate binding modes were sampled along each facet to study how different adsorbate and surface factors govern site preference. Adsorption energetics were then calculated using a DFT + thermodynamics approach which combines DFT energies with tabulated data and Nernst-based corrective terms to incorporate different experimental parameters.

FINDINGS

Instead of a universal trend, each facet displays a unique factor that dominates site preference based on either strain (001), functional groups (110), or topography (012). Adsorption energies predict favorable inner-sphere adsorption for both molecules but opposite energetic trends with varying pH. Additionally, vibrational analysis was conducted for each system and compared to experimental IR data. The work presented here provides an effective, computational methodology to study numerous adsorption processes occurring at the surface-aqueous interface.

Plasma-Functionalized Isotactic Polypropylene Assembled with Conducting Polymers for Bacterial Quantification by NADH Sensing

Rapid detection of bacterial presence on implantable medical devices is essential to prevent biofilm formation, which consists of densely packed bacteria colonies able to withstand antibiotic-mediated killing. In this work, a smart approach is presented to integrate electrochemical sensors for detecting bacterial infections in biomedical implants made of isotactic polypropylene (i-PP) using chemical assembly. The electrochemical detection is based on the capacity of conducting polymers (CPs) to detect extracellular nicotinamide adenine dinucleotide (NADH) released from cellular respiration of bacteria, which allows distinguishing prokaryotic from eukaryotic cells. Oxygen plasma-functionalized free-standing i-PP, coated with a layer (≈1.1 µm in thickness) of CP nanoparticles obtained by oxidative polymerization, is used as working electrode for the anodic polymerization of a second CP layer (≈8.2 µm in thickness), which provides very high electrochemical activity and stability. The resulting layered material, i-PP_f /CP² , detects the electro-oxidation of NADH in physiological media with a sensitivity 417 µA cm^-2 and a detection limit up to 0.14 × 10^-3 m, which is below the concentration of extracellular NADH found for bacterial cultures of biofilm-positive and biofilm-negative strains.

Competition between electron transfer and base-induced elimination mechanisms in the gas-phase reactions of superoxide with alkyl hydroperoxides

Understanding the mechanism responsible for peroxides decomposition is essential to explain several biochemical processes. The mechanisms of the intrinsic reactions between the superoxide radical anion (O2˙-) and methyl, ethyl, and tert-butyl hydroperoxides (ROOH, with R = Me, Et, and t-Bu) have been characterized to understand the mechanism responsible for peroxides decomposition. The reaction energy diagrams suggest a competition between the spin-allowed and spin-forbidden electron transfer (ET), and base-induced elimination (ECO2) mechanisms. In all cases, the spin-allowed ET mechanism describes formation of the ozonide anion radical (O3˙-), either complexed with an alcohol molecule or separated. For the O2˙-/MeOOH(EtOOH) reactions, HCO2- (MeCO2-) + H2O + HO˙ and OH- + CH2O(MeCHO) + HO2˙ products are associated with the spin-forbidden ET and ECO2 channels, respectively. On the other hand, for the reaction between O2˙- and t-BuOOH, the spin-forbidden ET route describes formation of the MeCOCH2- enolate (either separated or hydrated) along with the methyl peroxyl (MeO2˙) radical. In addition, the regeneration of O2˙-via spin-forbidden ET and ECO2 channels was also characterized from the decomposition of ROOH, yielding diols (CH2(OH)2 and MeCH(OH)2), aldehydes (CH2O and MeCHO), and oxirane (cyc-CH2CMe2O).

Water and Ion Transfer to Narrow Carbon Nanotubes: Roles of Exterior and Interior

Narrow carbon nanotubes (CNTs) desalinate water, mimicking water channels of biological membranes, yet the physics behind selectivity, especially the effect of the membrane embedding CNTs on water and ion transfer, is still unclear. Here, we report ab initio analysis of the energies involved in transfer of water and K⁺ and Cl^- ions from solution to empty and water-filled 0.68 nm CNTs for different dielectric constants (ϵ) of the surrounding matrix. The transfer energies computed for 1 ≤ ϵ < ∞ permit a transparent breakdown of the transfer energy to three main contributions: binding to CNT, intra-CNT hydration, and dielectric polarization of the matrix. The latter scales inversely with ϵ and is of the order 10²/ϵ kJ/mol for both ions, which may change ion transfer from favorable to unfavorable, depending on ion, ϵ, and CNT diameter. This may have broad implications for designing and tuning selectivity of nanochannel-based devices.

Boosting the performance by the water solvation shell with hydrogen bonds on protonic ionic liquids: insights into the acid catalysis of the glycosidic bond

Hydrogen-bonding (HB) of protonic ionic liquids induced by the water solvation shell is proposed to dominate in the acid catalysis of the glycosidic bond in hydrolysis.

Structures and relative stability of hydrated ferrous ion clusters and temperature effects

Structures of solvated ferrous ion clusters have been investigated in the singlet and quintet spin states of the ferrous ion. Relative stabilities of isomers are also discussed at different temperatures.

On the Role of Water as a Catalyst in Prebiotic Chemistry

In this manuscript we provide computational support to the catalytic role of water in all kinds of pseudopericyclic reactions operating in the reductive acid cycle, as well as in other metabolic processes. Water catalysis is not limited to those reactions where simple translocation of hydrogen atoms occurs, such as those represented by NuH+E→Nu-EH general equation. Indeed, water catalysis is more general and extremely important in tautomerization reactions of the type HX-Y=Z→X=Y-ZH, which operate in the reductive citric acid cycle and metabolic processes. Moreover, the comprehensive theoretical study reported herein illustrates that these reactions appear to behave as authentic enzyme-catalyzed reactions showing Michaelis-Menten behavior, however with the abnormal singularity that the concentration of the catalytic "water clusters" of different length and nature must be taken as a huge number. Overall, the results presented are suggestive of the workability of the so-called "metabolism first" proposal in a hot water world, as water catalysis eliminates the dilution problem frequently associated to this proposal.

A theoretical study on the pKa values of selenium compounds in aqueous solution

The pK_a values of different kinds of selenium compounds (R-SeH) were investigated by using the ωB97XD method with a SMD model.

Understanding Carbamate Formation Reaction Thermochemistry of Amino Acids as Solvents for Postcombustion CO2 Capture

The carbamate stability constant for a data set of 10 amino acids, having potential for being postcombustion CO₂ capture (PCC) solvents, has been calculated using various implicit and explicit solvation shell models. This work also includes an extensive study of gas-phase free energy and enthalpy for the amino acid carbamate formation reaction with the Hartree Fock method, density functional methods [B3LYP/6-311++G(d,p)], and composite methods (G3MP2B3, G3MP2, CBS-QB3, and G4MP2). Ideal PCC solvent properties require finding a profitable tradeoff between various thermodynamic and system optimization parameters. Benchmark gaseous-phase and solution-phase thermodynamic properties given in this work can help in making informed decisions when choosing promising PCC solvents. The temperature dependency of the carbamate stability constant of amino acids is predicted using PCM and SM8T implicit solvation models. PCC is a temperature swing absorption-desorption process, and the high-temperature sensitivity of the ln K_c^AmCOO- value is of vital importance in attaining cost-efficient processes.

Quantifying the Stability of the Hydronium Ion in Organic Solvents With Molecular Dynamics Simulations

The solution-phase stability of the hydronium ion catalyst significantly affects the rates of acid-catalyzed reactions, which are ubiquitously utilized to convert biomass to valuable chemicals. In this work, classical molecular dynamics simulations were performed to quantify the stability of hydronium and chloride ions by measuring their solvation free energies in water, 1,4-dioxane (DIOX), tetrahydrofuran (THF), γ-valerolactone (GVL), N-methyl-2-pyrrolidone (NMP), acetone (ACE), and dimethyl sulfoxide (DMSO). By measuring the free energy for transferring a hydronium ion from pure water to pure organic solvent, we found that the hydronium ion is destabilized in DIOX, THF, and GVL and stabilized in NMP, ACE, and DMSO relative to water. The distinction between these organic solvents can be used to predict the preference of the hydronium ion for specific regions in aqueous mixtures of organic solvents. We then incorporated the stability of the hydronium ion into a correlative model for the acid-catalyzed conversion of 1,2-propanediol to propanal. The revised model is able to predict experimental reaction rates across solvent systems with different organic solvents. These results demonstrate the ability of classical molecular dynamics simulations to screen solvent systems for improved acid-catalyzed reaction performance.

Effect of Side Chain Functional Groups on the DPPH Radical Scavenging Activity of Bisabolane-Type Phenols

Methods for improving the antioxidant activity of phenolic compounds have been widely investigated; however, most studies have focused on the structure⁻activity correlations of substituents on the aromatic rings of catechols or flavonoids. We investigated the influence of side chain functional groups on the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity of xanthorrhizol and curcuphenol analogues. These compounds were synthesised by the side chain functional group conversion of curcumene, followed by direct oxidation of the aromatic ring. We determined the DPPH radical scavenging activity from the half-maximal effective concentration (EC₅₀) obtained from a DPPH assay in methanol. The positional relationships of the side chain with the aromatic ring and phenolic OH group were determined using density functional theory calculations, and the stability of different conformations was compared. Electron transfer-proton transfer was determined to be the dominant mechanism in the DPPH reaction with xanthorrhizol analogues, based on the correlation between the EC₅₀ and ionisation potential. The radical cation was greatly stabilised in the structure where the side chain functional group was close to the aromatic ring. Stabilisation also depended on the phenolic OH group position. In future antioxidant design, aromatic ring substituent conversion and the use of functional groups far from the OH group or ring should be explored.

Ionic radii of hydrated sodium cation from QTAIM

The sodium cation is ubiquitous in aqueous chemistry and biological systems. Yet, in spite of numerous studies, the (average) distance between the sodium cation and its water ligands, and the corresponding ionic radii, are still controversial. Recent experimental values in solution are notably smaller than those from previous X-ray studies and ab initio molecular dynamics. Here we adopt a "bottom-up" approach of obtaining these distances from quantum chemistry calculations [full MP2 with the 6-31++G(d,p) and cc-pVTZ basis-sets] of gas-phase Na⁺(H₂O)_n clusters, as a function of the sodium coordination number (CN = 2-6). The bulk limit is obtained by the polarizable continuum model, which acts to increase the interatomic distances at small CN, but has a diminishing effect as the CN increases. This extends the CN dependence of the sodium-water distances from crystal structures (CN = 4-12) to lower CN values, revealing a switch between two power laws, having a small exponent at small CNs and a larger one at large CNs. We utilize Bader's theory of atoms in molecules to bisect the Na⁺-O distances into Na⁺ and water radii. Contrary to common wisdom, the water radius is not constant, decreasing even more than that of Na⁺ as the CN decreases. We also find that the electron density at the bond critical point increases exponentially as the sodium radius decreases.

On the Use of Thermodynamic Cycles for the Calculation of Standard Potentials for the Oxidation of Solid Metals in Solution

The performance of a thermodynamic cycle for the calculation of the standard reduction potential (SRP) of a series of metals is examined. It is found that the introduction of simple entropic corrections substantially improves the agreement with experimental data. The accuracy of the estimations is in the range of 0.04 V, which opens the possibility to calculate the SRP for metals in non-aqueous solvents or other unusual situations.

Theoretical modeling of pKa's of thiol compounds in aqueous solution

The pK_a's of different kinds of thiols (R-SH) were investigated by using the M06-2X method with a SMD_sSAS model.

Structure of the aqueous electron

A cavity or excluded-volume structure best explains the experimental properties of the aqueous or “hydrated” electron.

Solvation energies of the proton in methanol revisited and temperature effects

Various functionals assessing solvation free energies and enthalpies of the proton in methanol.

Computational study of Th(4+) and Np(4+) hydration and hydrolysis of Th(4+) from first principles

The aqueous solvation of Th and Np in the IV oxidation state was examined using cluster models generated by Monte Carlo simulations and density functional theory embedded within the COSMO continuum model to approximate the effect of bulk water. Our results suggest that the coordination number (CN) for both Th(IV) and NP(IV) should be 9, in accordance to some experimental and theoretical results from the literature. The structural values for average oxygen-metal distances are within 0.01 Å compared to experimental data, and also within the experimental error. The calculated ΔG _Sol⁰ are in very good agreement with experimental reported values, with deviations at CN = 9 lower than 1% for both Th(IV) and Np(IV). The hydrolysis constants are also in very good agreement with experimental values. Finally, this [corrected] methodology has the advantage of using a GGA functional (BP86) that not only makes the calculations more affordable computationally than hybrid functional or ab initio molecular dynamics simulations (Car-Parrinello) calculations, but also opens the perspective to use resolution of identity (RI) calculations for more extended systems.

Structures and spectroscopy of protonated ammonia clusters at different temperatures

Protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules.

Intrinsic Relative Stabilities of the Neutral Tautomers of Arginine Side-Chain Models

The specific protonation state of amino acids is crucial for the physicochemical properties of proteins and their biological functions. These protonation states influence, for instance, properties related to hydrogen bonding, solubility, and folding. pKa calculations for proteins are, therefore, important and require, in principle, a specification of the most stable protonated and deprotonated forms of each titratable group. This is complicated by the existence of multiple tautomers, like the five neutral tautomers of the guanidine moiety in arginine. In this study, the compounds N-methyl-guanidine and N-ethyl-guanidine were used to model the charged and all neutral protonation states of the arginine side chain. The relative stabilities of all five neutral tautomers were investigated systematically for the first time, using quantum-mechanical calculations. These relative stabilities were obtained in vacuo, water and chloroform, by combining the quantum-mechanical calculations with a continuum solvation model. The water model was used to represent arginines exposed to an aqueous solution, whereas the chloroform model has a polarity representative of a protein core or a membrane. This allowed determining the relative pKa's associated with each neutral tautomer in these environments. A key result is that significant differences in stability are found between the neutral tautomers, in both water and chloroform. Some tautomers are consistently found to be the most stable. These findings will be helpful to refine pKa calculations in proteins.

Incorporating excluded solvent volume and physical dipoles for computing solvation free energy

The solvation free energy described using the Born equation depends on the solute charge, solute radius, and solvent dielectric constant. However, the dielectric polarization derived from Gauss's law used in the Born equation differs from that obtained from molecular dynamics simulations. Therefore, the adjustment of Born radii is insufficient for fitting the solvation free energy to various solute conformations. In order to mimic the dielectric polarization surrounding a solute in molecular dynamics simulations, the water molecule in the first coordination shell is modeled as a physical dipole in a van der Waals sphere, and the intermediate water is treated as a bulk solvent. The electric dipole of the first-shell water is modeled as positive and negative surface charge layers with fixed charge magnitudes, but with variable separation distance as derived from the distributions of hydrogen and oxygen atoms of water dictated by their orientational distribution functions. An equation that describes the solvation free energy of ions using this solvent scheme with a TIP3P water model is derived, and the values of the solvation free energies of ions estimated from this derived equation are found to be similar to those obtained from the experimental data.

Predicting hydration energies for multivalent ions

We have predicted the free energy of hydration for 40 monovalent and multivalent cations and anions using density functional theory and the implicit solvent model COnductor like Screening MOdel for Real Solvents (COSMO-RS) at the Becke-Perdew (BP)/Triple zeta valence with polarization functions (TZVP) level. Agreement with experimental data for monovalent and divalent ions is good and shows no significant systematic errors. Predictions are noticeably better than with standard COSMO. The agreement with experimental data for trivalent and tetravalent ions is slightly worse and shows systematic errors. Our results indicate that quantum chemical calculations combined with COSMO-RS solvent treatment is a reliable method for treating multivalent ions in solution, provided one hydration shell of explicit water molecules is included for metal cations. The accuracy is not high enough to allow absolute predictions of hydration energies but could be used to investigate trends for several ions, thanks to the low computational cost, in particular for ligand exchange reactions.