Theoretical calculations on the basicity of amines

Competition and selectivity in supramolecular synthesis: structural landscape around 1-(pyridylmethyl)-2,2′-biimidazoles

Three isomeric forms of 1-(pyridylmethyl)-2,2′-biimidazole, A1–A3, have been synthesized and subjected to systematic co-crystallizations with selected hydrogen- and halogen-bond donors in order to explore the impact of electrostatics and geometry on the resulting supramolecular architectures. The solid-state supramolecular behavior of A1–A3 is largely consistent in halogen-bonded co-crystals. Only two types of primary interactions, the N–H⋯N/N⋯H–N homomeric hydrogen-bond interactions responsible for the pairing of biimidazole moieties and the I⋯N(pyridine) halogen bonds responsible for the co-crystal formation and structure extension, are present in these systems. The co-crystallizations with hydrogen-bond donors (carboxylic acids), however, lead to multiple possible structural outcomes because of the presence of the biimidazole–acid N–H⋯OC/N⋯H–O heterosynthon that can compete with biimidazole–biimidazole N–H⋯N/N⋯H–N homosynthon. In addition, the somewhat unpredictable nature of proton transfer makes the hydrogen-bonded co-crystals structurally less consistent than their halogen-bonded counterparts.

Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach.

Estimation of molecular acidity via electrostatic potential at the nucleus and valence natural atomic orbitals

An effective approach of estimating molecular pK(a) values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pK(a) values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pK(a) data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pK(a) values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules.

Predicting and Tuning Physicochemical Properties in Lead Optimization: Amine Basicities

This review describes simple and useful concepts for predicting and tuning the pK(a) values of basic amine centers, a crucial step in the optimization of physical and ADME properties of many lead structures in drug-discovery research. The article starts with a case study of tricyclic thrombin inhibitors featuring a tertiary amine center with pK(a) values that can be tuned over a wide range, from the usual value of around 10 to below 2 by (remote) neighboring functionalities commonly encountered in medicinal chemistry. Next, the changes in pK(a) of acyclic and cyclic amines upon substitution by fluorine, oxygen, nitrogen, and sulfur functionalities, as well as carbonyl and carboxyl derivatives are systematically analyzed, leading to the derivation of simple rules for pK(a) prediction. Electronic and stereoelectronic effects in cyclic amines are discussed, and the emerging computational methods for pK(a) predictions are briefly surveyed. The rules for tuning amine basicities should not only be of interest in drug-discovery research, but also to the development of new crop-protection agents, new amine ligands for organometallic complexes, and in particular, to the growing field of amine-based organocatalysis.

Quantifying the electronic effect of substituted phosphine ligands via molecular electrostatic potential

Values of the molecular electrostatic potential minimum (V(min)) corresponding to the lone pair region of several substituted phosphine ligands (PR(3)) have been determined at the DFT level. The V(min) value is proposed as a quantitative measure of the electronic effect of the PR(3) ligands. Good linear correlation between V(min) and Tolman electronic parameter of PR(3) has been obtained. V(min) is also proportional to the pK(a) values of the conjugate acids of PR(3), viz., [PR(3)H](+). Further, the DeltaE values of the reaction Ni(CO)(3) + PR(3) --> Ni(CO)(3)PR(3) and ScH(3) + PR(3) --> ScH(3)PR(3) are also linearly proportional to the V(min) values. However, if there is a strong metal to phosphorus pi-back-bonding, the DeltaE and V(min) do not fit to a line. It is also found that the standard reduction potential as well as the enthalpy change corresponding to the electrochemical couple eta-Cp(CO)(PR(3))(COMe)Fe(+)/eta-Cp(CO)(PR(3))(COMe)Fe(0) is linearly proportional to the V(min) values of PR(3). These correlations suggest that V(min) is a quantitative measure of the sigma-donating ability of the phosphine. It is hoped that, in phosphine-metal coordination chemistry, the V(min) based electronic parameter could be more advantageous than nu-CO and pK(a) based electronic parameters as it solely represents the inherent electronic property of the ligand.