Ann M. Schmiedekamp

Synthesis and characterization of a spin crossover iron(II)–iron(III) mixed valence supramolecular pseudo-dimer exhibiting chiral recognition, hydrogen bonding, and π–π interactions

Reaction of iron(II) and the 3 : 1 Schiff base condensate of 5-methylpyrazole-3-carboxaldehyde and tris(2-aminoethyl)amine in air gives a pseudo-dimer complex with a triple helix structure made of Δ–Δ and Λ–Λ pairings of spin crossover iron(II) and low spin iron(III) cations that are held together by three π–π and hydrogen bonding interactions.

Are aromatic carbon donor hydrogen bonds linear in proteins

Proteins fold and maintain structure through the collective contributions of a large number of weak, noncovalent interactions. The hydrogen bond is one important category of forces that acts on very short distances. As our knowledge of protein structure continues to expand, we are beginning to appreciate the role that weak carbon‐donor hydrogen bonds play in structure and function. One property that differentiates hydrogen bonds from other packing forces is propensity for forming a linear donor‐hydrogen‐acceptor orientation. To ascertain if carbon‐donor hydrogen bonds are able to direct acceptor linearity, we surveyed the geometry of interactions specifically involving aromatic sidechain ring carbons in a data set of high resolution protein structures. We found that while donor–acceptor distances for most carbon donor hydrogen bonds were tighter than expected for van der Waals packing, only the carbons of histidine showed a significant bias for linear geometry. By categorizing histidines in the data set into charged and neutral sidechains, we found only the charged subset of histidines participated in linear interactions. B3LYP/6‐31G**++ level optimizations of imidazole and indole–water interactions at various fixed angles demonstrates a clear orientation dependence of hydrogen bonding capacity for both charged and neutral sidechains. We suggest that while all aromatic carbons can participate in hydrogen bonding, only charged histidines are able to overcome protein packing forces and enforce linear interactions. The implications for protein modeling and design are discussed. Proteins 2008.

An ab initio study of the structures and the harmonic and anharmonic stretching force constants of the cyanides HCN, LiCN, FCN, ClCN and isocyanides HNC, LiNC, FNC, ClNC

Abstract Equilibrium structures and both harmonic and anharmonic stretching force constants have been calculated ab initio for the four cyanides HCN, LiCN, FCN, and C1CN, and the four isocyanides HNC, LiNC, FNC, and ClNC, using several basis sets of about triple-zeta quality. The CN and NC bond lengths, as well as diagonal stretching force constants, are nearly the same throughout both series. Trends in the off-diagonal stretching force constants are discussed, and dipole moment values are correlated with the structural type, XCN and XNC, and the electronegativity of the ligand X.

Triazene proton affinities: a comparison between density functional, Hartree-Fock, and Post-Hartree-Fock methods

The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high‐level Hartree–Fock and Møller–Plesset (MP) calculations for triazene (HNNNH2) and formyl triazene (HNNNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation.

Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function

Carbon donor hydrogen bonds are typically weak interactions that contribute less than 2 kcal/mol, and provide only modest stabilization in proteins. One exception is the class of hydrogen bonds donated by heterocyclic side chain carbons. Histidine is capable of particularly strong interactions through the Cepsilon(1) and Cdelta(2) carbons when the imidazole is protonated or bound to metal. Given the frequent occurrence of metal-bound histidines in metalloproteins, we characterized the energies of these interactions through DFT calculations on model compounds. Imidazole-water hydrogen bonding could vary from -11.0 to -17.0 kcal/mol, depending on the metal identity and oxidation state. A geometric search of metalloprotein structures in the PDB identified a number of candidate His C-H...O hydrogen bonds which may be important for folding or function. DFT calculations on model complexes of superoxide reductase show a carbon donor hydrogen bond positioning a water molecule above the active site.

Proton affinities of molecules containing nitrogen and oxygen: Comparing density functional results to experiment

SummaryProton affinities were calculated using density functional theory for 11 small molecules whose primary protonation site is on nitrogen, and eight small molecules that protonate on oxygen. Calculations were performed using both the local spin density approximation and nonlocal gradient corrections to the exchange correlation functional. The results were not sensitive to whether the nonlocal gradient correction was implemented on the final local spin density optimized geometry or whether the correction was included in the self-consistent calculation of the energy at each optimization step. Although negligible basis set dependence was found using the analytic Gaussian basis sets, numerical basis sets required augmentation by a double set of polarization functions to achieve reasonable agreement with experiment. All calculations systematically underestimated oxygen proton affinities.

A comparative ab initio study of the geometry and force field of thionformic acid with formic and thiolformic acids

Abstract The energy and force field for the planar cis and trans conformers of thionformic acid have been calculated using the 4–31 G basis set, augmented by a complete set of d -functions on the sulfur atom, with full geometry optimization. Extensive comparisons are made between the changes in geometry and selected force constants in going from cis - (chain) to the trans - (ring) structures of thionformic, thiolformic and formic acid. These changes are discussed in terms of a hydrogen bonding type of interaction in the OH⋯S, SH⋯O and OH⋯O structural units respectively. Of the thioacid conformers, the trans -thiol is found to be the most stable; the trans -thion and cis -thiol both about 10 kJ mol −1 less stable; and the cis -thion the least stable by about 38 kJ mol −1 .

Ab initio calculation of distortion and bonding energy components of the cis-trans conversion energy for formic, thiolformic and thionformic acids

Abstract The energy change in the formation of the intramolecular hydrogen-bonded ring conformers of formic, thiolformic and thionformic acids from the chain conformers has been divided up into distortion and bonding energy components, following the treatment of Smit, Derissen, and van Duijneveldt for the formation of the formic acid dimer.

Synthesis and characterization of seven-coordinate tripodal imidazole complexes of iron(II) and manganese(II)

The iron(II) and manganese(II) complexes of the N(7) Schiff-base condensate of tris(3-aminopropyl)amine with 1-methyl-2-imidazolecarbaldehyde and the manganese(II) complex of the N(7) Schiff-base condensate of tris(3-aminopropyl)amine with 4-imidazolecarbaldehyde are high-spin mono capped octahedral seven-coordinate complexes with a short, approximately 2.44 è, metal to apical nitrogen bond.

A DFT computational study of spin crossover in iron(III) and iron(II) tripodal imidazole complexes. A comparison of experiment with calculations

B3LYP* functionals were used to model the sixteen iron(II) (1A, LS and 5T, HS) and iron(III) (2T, LS and 6A, HS) complexes of the 1 : 3 Schiff base condensate of tris(2-aminoethyl)amine and imidazole-4-carboxaldehyde, H3L1, and its deprotonated forms, [H2L1]1-, [HL1]2-, and [L1]3-. This ligand system is unusual in that [FeH3L1]3+, [FeH3L1]2+ and [FeL1]- all exhibit a spin crossover between 100-300 K. This makes these complexes ideal for a hybrid DFT computational approach and provides an opportunity to refine the value of the exact exchange admixture parameter, c3, and to predict properties of partially protonated complexes that are not experimentally available. The accepted value of 0.20 is larger than the value of approximately 0.13 that was found to best reproduce experimental data in terms of spin state predictions. With iron(III) B3LYP calculations showed that all of the complexes were low spin at 298 K with the exception of [FeH3L1]3+ which is spin crossover in agreement with experimental results. It was also shown for iron(III) that the ligand field increased as the number of protons decreased. In contrast all of the iron(II) complexes were close to the spin crossover region regardless of protonation state. Experimental structures are fairly well modeled by this system in regard to the key structural indicators of spin state, which are the bite and trans angles. The calculated iron to nitrogen atom distances are always larger in the high spin form than the low spin form but all iron to nitrogen bond distances are larger than the experimental values. In general non-bonded interactions are not well modeled by this methodology.