Group Additivity Principle Research Articles

Structure–activity relationship for the estimation of OH-oxidation rate constants of carbonyl compounds in the aqueous phase

Abstract. In the atmosphere, one important class of reactions occurs in the aqueous phase in which organic compounds are known to undergo oxidation towards a number of radicals, among which OH radicals are the most reactive oxidants. In 2008, Monod and Doussin have proposed a new structure–activity relationship (SAR) to calculate OH-oxidation rate constants in the aqueous phase. This estimation method is based on the group-additivity principle and was until now limited to alkanes, alcohols, acids, bases and related polyfunctional compounds. In this work, the initial SAR is extended to carbonyl compounds, including aldehydes, ketones, dicarbonyls, hydroxy carbonyls, acidic carbonyls, their conjugated bases, and the hydrated form of all these compounds. To do so, only five descriptors have been added and none of the previously attributed descriptors were modified. This extension leads now to a SAR which is based on a database of 102 distinct compounds for which 252 experimental kinetic rate constants have been gathered and reviewed. The efficiency of this updated SAR is such that 58% of the rate constants could be calculated within ±20% of the experimental data and 76% within ±40% (respectively 41 and 72% for the carbonyl compounds alone).

Extending the group contribution concept using kihara potential to perfluorinated n-alkanes C nF 2 n+2 ( n = 1–6) for estimating thermophysical properties

The concept of the group contribution using Kihara intermolecular potentials with a spherical core is extended to perfluorinated n-alkanes ( n = 1–6). The effective Kihara parameters for groups (CF 2, CF 3, CF 4) are estimated by fitting second virial coefficient B and dilute gas viscosity η together. The assumption of regarding CF 4 molecule as a single group is preferable to other two approaches based on the principle of group additivity: a combination of F–(CF 3) and CF 3–(F) groups; a single C–(F) 4 group and four F–(C) groups. Application of the model shows that second virial coefficients are represented with better results than those of the Tsonopoulos correlation, and are comparable to the correlation of Dymond's group and the Hohm correlation. Feasibility of the present method to calculate dilute gas viscosities is proved by comparison with the Lucas method, the Hohm correlation, the correlation of Yaws, and the Simsci Data Bank. Mixture property calculations of the model are enhanced by including binary group interaction coefficients k ij,gc, determined from second cross virial coefficient data, and are more reliable than other correlations for second cross virial coefficients and mixture viscosities. Prediction results of binary diffusion coefficients, not supplied to the parameter evaluations, are in significant agreement with experimental data and are compared well with values obtained by means of the Fuller method. Results studied here would be of use when extended to halogenated paraffins and their mixtures.

Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added

Recent calorimetric measurements of the solvation enthalpies of some dipeptide analogs confirm our earlier prediction that the principle of group additivity is not valid for the interaction of the peptide group with water. We examine the consequences for understanding the properties of peptide solvation. A major consequence is that the current value of the peptide-solvation enthalpy, which is a basic parameter in analyzing the energetics of protein folding, is seriously wrong. Electrostatic calculations of solvation-free energies provide an estimate of the size and nature of the error. Peptide hydrogen exchange rates provide an experimental approach for testing the accuracy of the solvation-free energies of peptide groups found by electrostatic calculations. These calculations emphasize that ignoring electrostatic interactions with neighboring NHCO groups should be a major source of error. Results in 1972 for peptide hydrogen exchange rates demonstrate that peptide-solvation-free energies are strongly affected by adjoining NHCO groups. In the past, the effect of adjoining peptide groups on the exchange rate of a peptide NH proton was treated as an inductive effect. The effect can be calculated, however, by an electrostatic model with fixed partial charges and a continuum solvent.

Limited validity of group additivity for the folding energetics of the peptide group

The principle of group additivity is a standard feature of analyses of the energetics of protein folding, but it is known that it may not always be valid for the polar peptide group. The neighboring residue effect shows that group additivity is not strictly valid for a heteropeptide. We show here that group additivity fails seriously for peptide groups close to either peptide end, even for a homopeptide that has blocked end groups with no formal charges involved. The failure of group additivity is caused by the electrostatic character of the solvation of peptide polar groups and is illustrated with values of the electrostatic solvation free energy (ESF) calculated by DelPhi. Solvation free energies and enthalpies are known experimentally for monoamides and are often used to model the solvation of peptide groups, but ESF results show that monoamide values are very different from those of peptide groups. A main cause of the difference is that peptide solvation depends on the dipole-dipole interactions made between adjacent peptide groups, which vary with peptide conformation. Ligands that interact with the peptide backbone by an electrostatic mechanism could show a similar peptide end effect, and hydrogen exchange results from the literature confirm that exchange rates are position-dependent close to peptide ends.

Activity coefficients and thermodynamic parameters for RbCl/CsCl + amide (acetamide, propanamide, and n-butanamide) + water system at 298.15 K

Electromotive force (emf) of the chemical cell without liquid-junction K-ISE | RbCl/CsCl ( m E) | ISE-Cl and K-ISE | RbCl/CsCl ( m E), amide ( m N) | ISE-Cl, have been measured at 298.15 K, where m E = (0.005 to 0.5) mol kg − 1 and m N= (0.05 to 3.0) mol kg − 1 . The activity coefficients of RbCl/CsCl in amide (acetamide, propanamide, and n-butanamide) + water mixture can be obtained from these electromotive force data and in the mean time the Gibbs free energy interaction parameters of RbCl/CsCl + amide pair in water, g EN, as well as the salt constant, k S, can be evaluated. The results show that both g EN > 0, k S > 0 at 298.15 K, and all the activity coefficients of electrolyte in amide + water mixture increase with increasing the m N, but it is a little complicated for the dependence of activity coefficients on m E. These thermodynamic parameters were discussed in terms of a model of the structural interaction and electrostatic interaction and the dependence of them on the number of carbon atoms in amide as well as the radius of metal ions were interpreted by the group additivity principle.

Thermodynamics Study of the Interaction of CsCl with d-Glucose in Water from T = 278.15 to 313.15 K

Electromotive forces of cells without liquid junctions K-ISE | CsCl(mE) | ISE-Cl and K-ISE | CsCl(mE), glucose(mS) | ISE-Cl have been measured at 5 K intervals from T = 278.15 to 313.15 K, where mE = (0.001 to 0.1) mol kg-1 and mS = (0.01 to 3.0) mol kg-1. The activity coefficients of CsCl in glucose + water solutions can be obtained from these electromotive force data; in the meantime, the interaction parameters of the CsCl + glucose pair in water, gEN, hEN, sEN, and cp,EN, can be evaluated. We show that gEN > 0, hEN > 0, sEN > 0, and cp,EN < 0 at all four temperatures (except for hEN and sEN at T = 313.15 K), and the values of gEN, sEN, and cp,EN vary slightly with temperature, whereas the values of hEN is very sensitive to the temperatures used. These thermodynamic parameters were discussed in terms of a model of the structural interaction and electrostatic interaction and were analyzed by the group additivity principle.

Volumetric properties and volumetric interaction parameters for the CsCl–monosaccharide ( d-galactose, d-xylose and d-arabinose)–water systems at T=298.15 K

Density measurements have been carried out at T=298.15 K for the CsCl–monosaccharide ( d-galactose, d-xylose and d-arabinose)–water systems. The apparent molar volume of saccharides V φ,S in the ternary solutions, the corresponding infinite dilution apparent molar volume V φ,S ∘, and the standard transfer volume Δ t V φ,S ∘ of saccharides from water to aqueous CsCl solutions have been determined. The McMillan–Mayer theory was employed to relate the excess thermodynamic functions to a series of interaction parameters to obtain the volumetric interaction parameters of CsCl with monosaccharide in water. These parameters are interpreted by the group additivity principle and the stereochemistry of these monosaccharide molecules.

Hydrophobicity and Reactivity of Base Hydrolysis of Some Novel Low Spin Fe(II) Amino Acid Schiff Base Complexes in Some Binary Aqueous Solvent Mixtures

Rate constants for base hydrolysis of bis(naphthylidene isoleucinate)iron (II) (nili), bis(naphthylidene leucinate)iron(II) (nli), bis(naphthylidene serinate)iron(II) (nsi), bis(salicylidene isoleucinate)iron(II) (sili), (salicylidene leucinate)iron(II) (sli), bis(salic- ylidene methioninate)iron(II) (smi), and (salicylidene tryptophanate)iron(II) (sti) have been reported in different binary aqueous mixtures at 298 K. The observed reactivity trends are discussed in terms of the hydrophilic and hydrophobic forms of the complexes investigated, as well as the transfer chemical potentials of hydroxide ion and the complex. Both the solvent–solute and solvent–solvent interactions have been considered. The hydrophobic character of the complexes studied was manifested by enhancing the rate of base hydrolysis at the initial addition of the different cosolvents; further addition led mostly to a decrease in reactivity, but, in some cases, the greater destabilization of OH− ion by added DMSO and acetone increases the rate of base hydrolysis. The modified Savage–Wood equation, based on the principle of group additivity, was applied to estimate the observed kinetic medium effects.

Volumetric Properties and Volumetric Interaction Parameters of the CsCl‐saccharides (D‐glucose, D‐fructose)‐water Solutions at 298.15 K

AbstractDensities have been measured for the CsCl‐saccharide (D‐glucose, D‐fructose)‐water systems at 298.15 K. These data were used to calculate the apparent molar volume of CsCl (Vφ,E) and the saccharides (Vφ,S), and the infinite dilution apparent molar volume Vφ,E0 and Vφ,S0 in the studied solutions. In addition, the standard transfer volume ΔtVφ,E0 of CsCl from water to aqueous saccharides solutions, and ΔtVφ,S0 of saccharides from water to CsCl solutions have been evaluated and discussed using the structural interaction model. The volumetric interaction parameters for CsCl with saccharide in water were obtained and analyzed by the group additivity principle and the stereochemistry of the saccharide molecules.

Solvation and Enthalpy Coefficients of Interaction of Carboxylic Acid Amides with 1,2-Diols in Water

The enthalpies of solution of formamides, acetamides, and propionamides with various extents of N-substitution in aqueous solutions of propylene glycol and 1,2-butanediol (concentration ≤4 mol kg- 1) at 298.15 K were measured. The enthalpies of transfer of the amides from water to mixed aqueous-organic solvents were determined and discussed in combination with data on the enthalpies of transfer of amides from water to aqueous ethylene glycol solutions. The enthalpy coefficients of pair interactions of amides with 1,2-diols in water were calculated and used for evaluating the group components on the basis of the principle of group additivity of contributions. As the hydrophobic properties of polyfunctional nonelectrolytes are enhanced, the coefficients increase, which is due to the growth of the hydrophobic component of the interaction.

Interactions of HCl with 1-Butanol and Group Additivity Analysis for the HCl–Alcohol Interactions

An electromotive force (emf) method was used to determine thermodynamic parameters of interaction of HCl with normal 1-butanol (n-BuOH) in water between 5 and 45°C. A comparison of pair interaction parameters for HCl–n-BuOH with those for HCl–t-BuOH (tert butyl alcohol) showed that there is an obvious difference between them. This was interpreted in terms of steric structure of their carbon chains. The group Gibbs free energy parameters (\(G_{HCl} - {CH}_{2} \) and \(G_{HCl} - {OH} \)) for the HCl–alcohol–water systems were derived according to the Savage–Wood group additivity principle. These group parameters can be used to evaluate pair interaction parameters of HCl with alcohol molecules.

Additivity of the partial molar heat capacities of the amino acid side-chains of small peptides: Implications for unfolded proteins

The partial molar heat capacities at infinite dilution, Cp,20, for eight tetrapeptides of sequence glycyl–X–Y–glycine and four pentapeptides of sequence glycyl–X–Y–Z–glycine, where X, Y and Z are amino acids with neutral side-chains, have been determined in aqueous solution over the temperature range 283.15 to 373.15 K using high sensitivity scanning microcalorimetry. The results are compared with those calculated by group additivity using the partial molar heat capacities for the constituent groups of unfolded proteins that we reported in previous work. The comparison verifies that the heat capacity of a polypeptide with neutral side-chains can be reliably estimated using the principle of group additivity and our published group heat capacities.

The partial molar volumes of some tetra- and pentapeptides in aqueous solution: a test of amino acid side-chain group additivity for unfolded proteins

Ten new peptides with the amino acid sequences glycyl-X-Y-glycine and glycyl-X-Y-Z-glycine, where X, Y and Z are amino acids with neutral side-chains, have been synthesized and the partial molar volumes at infinite dilution, V2°, have been determined for all these peptides in aqueous solution at 298.15 K. For several of the peptides, V2° data have also been obtained over the temperature range 283.15 to 363.15 K using a scanning densimetric method. The V2° results obtained are compared with those calculated using the principle of group additivity and the group partial molar volumes we have derived in earlier work. We have shown that our group partial molar volumes can be used to reliably predict the partial molar volumes over a wide temperature range of polypeptides that have neutral amino acid side-chains.

Thermodynamics of the interaction of HCl with d-arabinose in water at 278.15–318.15 K

The thermodynamic parameters of interaction of HCl with d-arabinose in water were determined from electromotive force measurements from 278.15 to 318.15 K. The standard Gibbs free energies of transfer of HCl from water to aqueous solutions of 5, 10, and 15 wt.% of d-arabinose were evaluated. The group interaction Gibbs free-energy parameters ( G HCl–CH 2 , G HCl–OH, G HCl– e-OH , G HCl– a-OH , and G HCl–O) for the HCl–sugar (or alcohol)–water systems were evaluated and discussed in terms of the Savage–Wood group additivity principle and the stereochemistry of sugars, where –OH, – e-OH and – a-OH stand respectively for alcohol-, equatorial- and axial-hydroxyl groups. Of the five group interactions, the HCl– e-OH interaction contributes a large positive value to the pair interaction Gibbs free-energy parameters of HCl with sugars, whereas the contributions of the HCl– a-OH and HCl–O interactions are very small.

Reactions of HSCH2 Radical with O2, NO, and NO2: Ab Initio Calculations of Enthalpies of Reaction

For reactions of the HSCH2 radical with atmospheric gases O2, NO, and NO2, we describe the thermochemistry by HF, MP2, and density functional computational methods, by Petersson's complete basis set extrapolation (CBS-4 and CBS-Q), and, in part, by Pople's G2MP2 model chemistry method. We offer recommendations of values of heats of formation for the participants in these reactions, which differ in some cases from the estimates based on the group additivity principle. The least expensive post-Hartree−Fock methods provide a coherent account of the thermochemistry, but are not superior to group additivity estimation.

Apparent molar volumes of aqueous solutions of some organic solutes at the pressure 28 MPa and temperatures to 598 K

Densities of aqueous solutions of 16 organic electrolytes and polar solutes containing different functional groups at molality m≈ 0.12 mol·kg −1have been measured at temperatures T= (298.15, 373.15, 448.15, and 523.15 K) and at pressure p= 28 MPa. Densities of three of the solutions were also determined at T= 598.15 K. Partial molar volumes at infinite dilution V 2 ∞and p= 28 MPa were calculated for each of the solutes at the various temperatures and the results used to evaluate group contributions to V 2 ∞of the functional groups: CH 3- , CH 2-, -CONH 2, -COOH, -OH, and -NH 2. The V 2 ∞for most of the nonelectrolytes appear to be diverging in a positive direction at the higher temperatures, while V 2 ∞for the electrolytes diverges in a negative direction. Temperature dependencies of V 2 ∞for the solutes were analyzed in terms of four different semi-empirical equations employing temperature and temperature-dependent properties of water as variables. Parameters for each solute for the four equations are tabulated along with the standard deviations of the fits. All four equations reproduce the results reasonably well within the range of the measurements, but diverge widely above the temperature limits of the measurements. Two of the four equations have been fitted in the group volumes. These equations, along with the group additivity principle, were used to reproduce V 2 ∞of the original electrolytes over the entire range of temperatures, showing that the group additivity principle is useful to at least T= 523 K. This suggests that these equations may be used to give reasonable estimates of V 2 ∞from T= 298.15 K to T= 523 K for any aqueous organic solute which can be constructed from the six functional groups for which V 2 ∞s now exist.

Comparison of metal-hydrogen, -oxygen, -nitrogen and -carbon bond strengths and evaluation of functional group additivity principles for organoruthenium and organoplatinum compounds

The equilibria: L n MX + HY ⇁ L n MY + HX (L n M = (DPPE)MePt or Cp(PMe 3) 2Ru; X, Y = hydride, alkoxide, hydroxide, amide, alkyl, alkynyl, hydrosulphide, cyanide) have been examined. The equilibrium constants allow for the determination of relative MX, MY bond dissociation energies (BDEs) for each series of compounds. A linear correlation of L n MX to HX BDEs is found for the two dissimilar metal centres. Activation barriers for phosphine dissociation from Cp(PMe 3) 2RuX complexes have been measured and suggest the principle of functional group additivity has limited applicability in organometallic thermochemistry. The generality and predictive value of this correlation and the observations on functional group additivity are discussed.

Aqueous solutions containing amino acids and peptides. Part 22 - free energetic and enthalpic virial coefficients at 25�C for some interactions of isofunctional amides

The excess free energies of aqueous solutions containing N-acetyl-L-prolinamide, N-acetyl-N-methyl-L-alaninamide and binary mixtures of these have been determined at 25°C from isopiestic measurements. The corresponding excess enthalpies for the last two systems have been obtained from enthalpy of dilution measurements. The results derived have been considered using the Savage-Wood group additivity principle, and it is shown that this works remarkably well although deviations are observed which are probably significant.

Interactions in aqueous nonelectrolyte systems. Gibbs energy of interaction of the ether group with the hydroxyl group and the amide group

Freezing temperatures of dilute aqueous solutions of equimolar mixtures of 1,3,5-trioxane with myo-inositol, d-mannitol, cyclohexanol, formamide, and acetamide, and 1,4-dioxane with myo-inositol, d-mannitol, formamide, and acetamide have been measured. These data yield pairwise Gibbs energies of interactions between the molecules in an aqueous solution. Using the group additivity principle, the results also yield the pairwise functional group Gibbs energies of interaction for the ether group with the hydroxyl and amide group. These results have been combined with all available data from the literature to yield the Gibbs energy and enthalpy of interaction of amides, ethers, alcohols, and saccharides in aqueous solution.

Freezing temperatures of aqueous solutions of mixtures of amides and polyols. Gibbs energy of interaction of the amide group with the hydroxyl group in aqueous solution

Freezing temperatures of dilute aqueous mixtures of: formamide with myo-inositol, d-mannitol, and cyclohexanol; N,N-dimethylformamide with inositol, mannitol, and cyclohexanol; and acetamide with inositol and mannitol have been measured. These data have been analyzed to yield the pairwise molecular Gibbs energies of interaction between the molecules in an aqueous solution. Using the group additivity principle, the results yield the pairwise functional group Gibbs energies of interaction of the amide group with the hydroxyl group, GOH,CONH=−31 J-kg-mol−2.