Correlations and predictions of pKa values of fluorophenols and bromophenols using hydrogen-bonded complexes with ammonia

Density functional theory calculations have been preformed on a series of the hydrogen-bonded fluorophenol-ammonia and bromophenol-ammonia complexes. Intermolecular and intramolecular properties, particularly those related to hydrogen bonding, have been carefully analyzed. Several properties, such as the bond length and stretching frequency of the hydroxyl group, the hydrogen bond length and binding energy, are shown to be highly correlated with each other and are linearly correlated with known experimental pKa values of the halogenated phenols. The linear correlations have been used to predict the pKa values of all fluorophenols and bromophenols in the series. The predicted pKa values are shown to be consistent from different molecular properties and are in good agreement with available experimental values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow the effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations.     

Correlations and predictions of carboxylic acid pKa values using intermolecular structure and properties of hydrogen-bonded complexes

Density functional theory calculations have been preformed on a series of hydrogen-bonded complexes of substituted aliphatic and aromatic carboxylic acids with ammonia. Molecular properties, particularly those related to hydrogen bonding, have been carefully examined for their interdependence as well as dependence on the acidity of the acid. The bond length and stretching frequency of the hydroxyl group and the hydrogen-bond length and energy of the complex are shown to be highly correlated with each other and are linearly correlated with available literature pKa values of the carboxylic acids. The linear correlations resulting from the fit to the available pKa values can be used to predict the pKa values of similar carboxylic acids. The pKa values so predicted using the different molecular properties are highly consistent and in good agreement with the literature values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations. This approach is unique in its capability to determine the acidity of a particular functional group or the local acidity within a large molecular system such as a protein.     

Theoretical investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes

Systematic investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes has revealed that fluorobenzene, difluorobenzene, and trifluorobenzene favor formation of cyclic complexes with a C-H...N-H...F-C binding motif. On the other hand, tetrafluorobenzene and pentafluorobenzene favor formation of linear C-H...N hydrogen-bonded complexes. The complete absence of exclusively linear N-H...F hydrogen-bonded complexes for the entire series indicates that C-F bond in fluorobenzenes is a reluctant hydrogen-bond acceptor. However, fluorine does hydrogen bond when cooperatively stabilized with C-H...N hydrogen bonds for the lower fluoro analogues. The propensity of fluorobenzenes to adapt to the C-H...N-H...F-C binding motif decreases with the progressive fluorination of the benzene ring and disappears completely when benzene ring is substituted with five or more fluorine atoms.     

Theoretical study of hydrogen-bonded formaldehyde complexes

The hydrogen-bonded complexes involving formaldehyde and a series of proton donors of varying strengths, have been investigated at different levels of ab initio MO theory. The structures of the studied complexes were SCF optimized at the 6-31G basis set level. The binding energy was estimated employing basis set superposition correction, zero-point vibrations and MP2 correlation contribution at the different basis set: STO-3G; 6-31G; MP2/6-31G; 6-31G**; MP2/6-31G**; 6-311G(2d, 2p) and MP2/6-311G(2d, 2p). Linear relationships were found of the calculated binding energy with: the calculated shift in the carbonyl stretching frequency, the changes in carbonyl bond length and the optimum value of hydrogen-bond distance; furthermore the calculations confirm a parallel trend between the proton-donor ability and the strength of the hydrogen bond.     

Theoretical study of the structure, stability, and infrared spectra of hydrogen-bonded complexes of N-nitrosodiethanolamine (NDELA) with water molecules

A theoretical study of the interaction between the N-nitrosodiethanolamine (NDELA) molecule and one to five water molecules was performed at the B3LYP level using a large polarized basis set. The calculated complexation energies (corrected for BSSE and ZPVE) of NDELA with one, two, three, four, and five water molecules are ?4.62 kcal/mol, ?9.83 kcal/mol, ?15.29 kcal/mol, ?21.60 kcal/mol, and ?25.10 kcal/mol respectively at the B3LYP/6-311++G** level. In all complexes studied, there are red shifts in the vibrational frequencies of the O-Hs of NDELA and water molecules along with increases in the corresponding IR intensities.     

Ab initio molecular orbital calculations of the infrared spectra of hydrogen-bonded complexes of water,ammonia and hydroxylamine

Summary The geometries of three hydrogen-bonded dimers of hydroxylamine have been optimized, at the MP2 level of theory, using the 6-31G** basis set. These calculations yielded three separate local minima on the dimer potential energy surface. The interaction energies of these three species have been calculated, and corrected for basis set superposition error. The infrared band wavenumbers and intensities have been computed, and the monomer-dimer wavenumber shifts and intensity enhancements rationalized in terms of the types and strengths of hydrogen bonds present. The predicted wavenumbers have been correlated with those measured in a recent matrix isolation spectroscopic study, and an argument for the structure of the preferred dimer has been presented.     

Theoretical study of ammonia nucleophilic addition to nitriles in platinum complexes

The mechanism of the reaction of the ammonia nucleophilic addition to nitriles RC≡N, both free and activated in the platinum complex trans-[PtCl₂(N≡CCH₃)₂], was studied in detail by theoretical quantumchemical methods. The reaction resulting in the formation of free or coordinated amidines proceeds through consecutive formation of an orientation complex, a six-membered cyclic transition state, and a final reaction product, in which an amidine is in the E-configuration. Water containing in a solvent plays a role of a promoter of this process. The activation effect is interpreted from the viewpoint of both kinetic and thermodynamic factors. It was shown that the mechanism of the reaction product E-Z-isomerization includes the deprotonation of the amino-group nitrogen atom, the change of the coordinated ligand conformation, and the protonation of the nitrogen atom.     

Hyperpolarizabilities of hydrogen-bonded complexes of phenol derivatives with ammonia: PM3 and ab initio studies

Polarizability and first hyperpolarizability values of the hydrogen-bonded complexes formed by nitrosubstituted phenols with ammonia have been calculated using PM3 and ab initio (STO-3G) methods. It has been shown that enhancement of the polarizability (Δα) as well as the first hyperpolarizability (Δβ) of the complex arises from the hydrogen bond interaction between the phenol derivative and ammonia.     

Theoretical calculation of the pKa values of some drugs in aqueous solution

In this work, calculations of pK_a values have been performed on benzoic acid and its para‐substituted derivatives and some drugs by using Gaussian 98 software package. Gas‐phase energies were calculated with HF/6‐31 G** and B3LYP/6‐31 G** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor‐like PCM (CPCM), and the integral equation formalism‐PCM at the same levels which have been used for geometry determination in the gas‐phase. The results that show the calculated pK_a values using the B3LYP are better than those using the corresponding HF. In comparison to the other models, the results obtained indicate that the PCM model is a suitable solvation model for calculating pK_a values. For the investigated compounds, a good agreement between the experimental and the calculated pK_a values was also observed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Review: Bilirubin pKa studies; new models and theories indicate high pKa values in water,dimethylformamide and DMSO

Background  

Unconjugated bilirubin (UCB) is an unstable substance with very low aqueous solubility. Its aqueous pKa values affect many of its interactions, particularly their pH-dependence. A companion paper shows that only our prior solvent partition studies, leading to pKa values of 8.12 and 8.44, met all essential requirements for valid pKa determinations. Other published values, generally lower, some below 5.0, were shown to be invalid. The present work was designed to derive suitable models for interpreting published data on the pH-dependent binding of UCB with four agents, mentioned below, chosen because they are not, themselves, sensitive to changes in the pH range 4-10, and the data, mainly spectrometric, were of reasonable quality.     

pKa of acetate in water: a computational study

Several computational methods including the conductor-like polarizable continuum model, CPCM with both UAKS and UAHF cavities, Cramer and Truhlar's generalized Born solvation model, SM5.4(AM1), SM5.4(PM3), and SM5.43R(mPW1PW91/6-31+G(d)), and mixed QM/MM-Ewald simulations were used to calculate the pK(a) values of acetate and bicarbonate anions in aqueous solution. This work provided a critical and comprehensive assessment of the quality of these theoretical models in the calculation of aqueous solvation free energies for the singly charged acetate and bicarbonate ions, as well as the doubly charged acetate dianion and carbonate dianion. It was shown that QM/MM-Ewald simulations could give an accurate and consistent evaluation of the pK(a) values of acetate and bicarbonate based on both the relative and absolute pK(a) formulas, while other methods could yield satisfactory results only for certain calculations. However, this does not mean that the current QM/MM-Ewald protocol is superior to other methods. The useful information obtained in this investigation is that both the absolute and relative pK(a) formulas should better be tested in accurate calculations of pK(a) values based on any methods.     

Infrared spectroscopic study of hydrogen-bonded complexes of triphenylcarbinol and triphenylsilanol with ethers

Hydrogen bonding between triphenylcarbinol and triphenylsilanol with eight ethers of different types was investigated. Shifts of OH frequencies of the formed complexes were recorded in dilute CCl₄ solutions of the components. The observed shifts were correlated with the nucleophilicity parameters of the ethers, with their polarity and polarizability factors, their pK_a values and association constants of the ether-‘ol’ complexes. The silanol-ether interaction is perceptibly stronger than the ether-carbinol one. The acid-base mechanism in the interactions dominates, but polar and steric factors play a significant role in some cases.     

Theoretical study on cooperative and extra-additive behavior of hydrogen-bonded clusters

The stabilization energy △ E(n) and four typical properties of hydrogen bond F-H…F in chain-like and cyclic (HF)n clusters (n = 1-5) have been calculated using MP2 and three DF levels of theory with the Gaussian 98 program, and 6-31++G** bases set. The results demonstrate that the extra-additive or cooperative behavior in (HF)n clusters is very obvious. In addition, we studied much larger chain-like (HF)n (n = 6, 9, 12,18, 24) clusters using one of these DF methods.     

Quantum-chemical study of thermodynamics of hydrogen-bonded methylamine-methanol complexes reaction with dimethyl carbonate

Thermodynamic parameters of the reactions of dimethyl carbonate cis-cis and cis-trans conformers with methylamine, methylamine dimer, and methylamine complexes involving linear methanol associates have been computed with the B3LYP and WB97XD quantum-chemical methods. The both methods have given similar results. Thermodynamically, reactions of the cis-trans conformer are preferred over the analogous reactions of the cis-cis conformer, and the reactions with methylamine dimer and methylamine-methanol trimer complex are preferred over the reactions with methylamine monomer. The acid-base properties of the hydrogen-bonded methanol complexes are significantly enhanced with increasing degree of association. Stability of the methylamine complexes with methanol clusters is increased with more of the alcohol molecules involved.     

SN2-like reaction in hydrogen-bonded complexes: a theoretical study

S(N)2-like reactions in hydrogen-bonded complexes have been investigated in this paper at a correlated MP2(full)/6-311++G(3df,3pd) level, employing FH...NH(3)...HF and ClH...NH(3)...HCl as model systems. The unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond can coexist in one complex which is taken as the reactant of the S(N)2-like reaction. The S(N)2-like reaction occurs along with the inversion of NH(3) and the interconversion of the unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond. In comparison with that of the isolated NH(3), the inversion barriers of the two complexes both are significantly reduced. The effect of carbon nanotube confinement on the inversion barrier is also discussed.     

A theoretical study of nonlinearity in heterocyclic hydrogen-bonded complexes

Ab initio calculations are performed at the MP2/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) theoretical levels to obtain geometries, H-bond energies and harmonic infrared vibrational properties for the Cs symmetry structures of heterocyclic hydrogen-bonded complexes, CnHmY-HX. The H-bond lengths in DFT/B3LYP calculation level are in better agreement with the experimental values than the MP2 results. The geometry optimization are interpreted in terms of hydrogen bond nonlinearity represented by theta; and phi angles, once the hydrogen bond is formed among n-electrons pairs of the heteroatom in heterocyclic and the hydrogen atom in HX. The hydrogen bond energy after of the zero-point vibrational energy (ZPE) and basis set superposition error (BSSE) corrections are overestimated at DFT/B3LYP, whereas the MP2 BSSE corrections are very large than corresponding DFT/B3LYP. For example, the BSSE corrections for the C2H4S-HNC complex are 7.60 and 0.09 kJ mol(-1) in MP2 and DFT/B3LYP calculations levels, respectively. The new vibrational modes in infrared harmonic spectrum arising from complexation show several interesting features, especially the intermolecular stretching mode.     

Theoretical study of the ammonia trimer

Open-chain (I) and cyclic (II) structures of the ammonia trimer (NH₃)₃ have been optimized using the 4-3IG extended basis set. The- cyclic structure (II) is found to be the most stable, in agreement with recent experimental results.     

Theoretical predictions of the spectroscopic parameters in noble-gas molecules: HXeOH and its complex with water

We employ state-of-the-art methods and basis sets to study the effect of inserting the Xe atom into the water molecule and the water dimer on their NMR parameters. Our aim is to obtain predictions for the future experimental investigation of novel xenon complexes by NMR spectroscopy. Properties such as molecular structure and energetics have been studied by supermolecular approaches using HF, MP2, CCSD, CCSD(T) and MP4 methods. The bonding in HXeOH···H(2)O complexes has been analyzed by Symmetry-Adapted Perturbation Theory to provide the intricate insight into the nature of the interaction. We focus on vibrational spectra, NMR shielding and spin-spin coupling constants-experimental signals that reflect the electronic structures of the compounds. The parameters have been calculated at electron-correlated and Dirac-Hartree-Fock relativistic levels. This study has elucidated that the insertion of the Xe atom greatly modifies the NMR properties, including both the electron correlation and relativistic effects, the (129)Xe shielding constants decrease in HXeOH and HXeOH···H(2)O in comparison to Xe atom; the (17)O, as a neighbour of Xe, is deshielded too. The HXeOH···H(2)O complex in its most stable form is stabilized mainly by induction and dispersion energies.     

Intra- and intermolecular hydrogen bonding in formohydroxamic acid complexes with water and ammonia: infrared matrix isolation and theoretical study

The complexes of formohydroxamic acid with water and ammonia have been studied using FTIR matrix isolation spectroscopy and MP2 calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the HCONHOH/H₂O(NH₃)/Ar matrixes indicates formation of strongly hydrogen-bonded complexes in which the NH group of formohydroxamic acid acts as a proton donor toward the oxygen atom of water or the nitrogen atom of ammonia. The NH stretching vibration of formohydroxamic acid exhibits 150 cm⁻¹ red shift in the complex with water and 443 cm⁻¹ red shift in the complex with ammonia as compared to the NH stretch of the HCONHOH monomer. The theoretical calculations indicate stability of five isomers for the water complex and three isomers for the ammonia complex. The most stable are the cyclic structures in which the water or ammonia molecules are inserted within the intramolecular hydrogen bond of the formohydroxamic acid molecule and act as proton donors for the CO group and proton acceptors for the OH group of the formohydroxamic acid molecule. In spite of their stability the cyclic structures have not been observed in the matrixes which indicates high energy barrier for their formation, the reaction of complex formation is under kinetic and not thermodynamic control.