Ab Initio and Molecular Mechanics (MM3) Calculations of Protonated−Neutral Diamine Hydrogen Bonds

Abstract

Ab initio calculations of cation-neutral diamine complexes have been carried out at the MP2/6-311+G** level. The geometry and energetics of the charge-reinforced hydrogen bond are analyzed with respect to the alkyl substitution of both the protonated and neutral nitrogen atoms, and these results have been used to improve the quality of the MM3(2000) force field. In addition, specialized hydrogen bond parameters optimized for MM3(2000) are presented. These parameters allow very accurate gas-phase modeling of the charge-neutral diamine environment. Molecular mechanics calculations can model effectively protonated amine-neutral amine hydrogen bonds in the gas phase and solution (continuum dielectric) through a combination of charge-dipole interactions and explicit hydrogen-bonding terms.

pKa Calculations of Aliphatic Amines, Diamines, and Aminoamides via Density Functional Theory with a Poisson−Boltzmann Continuum Solvent Model

“…Conversely, it becomes weaker with the replacement of the two amino hydrogen atoms by methyl groups. A similar trend has been observed for the electronic binding energies of complexes of protonated amines with neutral amines . In the aqueous phase, the lowest-energy forms of the neutral diamines [see 11(aq) − 17(aq) in Figure ] are structurally similar and correspond to all-trans conformations.…”

Time-Resolved Fluorescence Anisotropy in Assessing Side-Chain and Segmental Motions in Polyamines Entrapped in Sol−Gel Derived Silica

“…This result could also be related to the existence of protonated−neutral diamine hydrogen bonds in PAM, which will slow both side-chain and segmental motions. According to ab initio calculations of cation−neutral diamine complexes, there are still strong interactions between charged and neutral amines at an internuclear distance of 4 Å. Hence, the molecular modeling results provide very clear and plausible evidence for the higher conformational flexibility of PL as compared to PAM.…”

Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1

“…A series of PCB structures was built and energy minimized, first with molecular mechanics using the MM3 force field (Allinger et al, 1989;Sorensen et al, 2001), and then using the semiempirical AM1 method (Dewar et al, 1985). The resulting geometries were similar to those obtained by ab initio methods using Gaussian94.…”