The Smallest Biomolecules: Diatomics and their Interactions with Heme Proteins

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Inorganic Chemistry For Dummies The simple method to get a grip on inorganic chemistry Inorganic chemistry may be an intimidating topic, however it does not must be! The oxygen atom populations were reproducible at a given temperature indicating the reversibility of the solid-state motion. The two minima seen in Figure 3 are the result of the NO ligand bracketed by peripheral p -fluorophenyl groups from different adjacent molecules. We have further examined the nature of the nonbonded contacts by calculating the potential energy using the semi-empirical nonbonded potential functions as originally outlined by Giglio 25 and expanded by Shmueli and Goldberg.

The results for the and K structures are displayed in Figure 4a. The potential energy plots are similar to those of the simpler svdWro summation plots. An important difference is that the energy differences between the two minima are apparently smaller. The energy difference between the two minima at K, a point for subsequent discussion, is 6. The success of this analysis led us to examine several additional six-coordinate samples. A total of six different compounds involving a total of 23 independent structure determinations at temperatures ranging from to K have now been used in this study.

NO motion ranges from movement between quite discrete positions to disorder best described by a continuum of positions over an angular range. However, the svdWro analysis Figure S2 suggests that this crystalline species could display a disordered NO at higher temperatures. Crystal structure determinations at and K confirm this prediction, with the population of the second position temperature dependent see Table 1.

The potential energy plots at and K Figure 4b show similar behavior but again suggest that the svdWro plots exaggerate the barrier between the two oxygen positions. The potential energy plot suggests greater accessibility of a second NO position, indeed this second position could actually be best represented by a continuum of NO positions. This is consistent with the extended motion of the second O1b position as shown by the thermal ellipsoids in Figure 5.

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The methyl group of imidazole is shown as the brown atom. The potential energy plot Figure 4c shows a broad minimum in which the valley becomes broader with increasing temperature. However, determining a minimal population of oxygen is limited by the detection limits of the X-ray diffraction experiment. This is especially problematic when determining if a site is unpopulated. The K structure of mono -[Fe T p FPP NO 1-MeIm ] was refined with the two oxygen positions having equal thermal parameters to better calculate the populations of each of the two sites. The statistical parameters are similar for both the constrained and unconstrained models.

R 1 wR 2 for the constrained and unconstrained models are 0. Additionally, the more extensive data set has provided evidence of a third NO orientation at K.

The plots show two distinct minima for both temperatures, but do not predict the positions of the NO oxygen atoms well. The potential energy plot Figure 4d however show that there is a broad region where the the location of the NO is favorable. This region at K has two very broad minima that become even broader at K. Alternate views of the complete molecule at the two temperatures are given in the Supporting Information Figure S8.

It is apparent from the thermal ellipsoids of the oxygen atoms at K that there is electron density between the two modeled positions resulting from unresolved NO positions. The statistical parameters were similar for both a three NO position model and two NO position model at K. The molecules are oriented with the plane of the porphyrins in the page to emphasize the orientations of NO oxygens.

However, the temperature-dependent changes in the intermolecular interactions are different from the previously analyzed systems. There are two well-defined minima; however the deeper of the two minima is exchanged on warming.

The potential energy plot Figure 4e also shows this behavior with a reversal of the more favorable minimum on change in temperature. We judge that the temperature-dependent population increase is somewhat larger than those seen in other examples. Both plots suggest that the NO position is rather tightly constrained at either temperature.

The nature of the interactions involving the NO ligand are different from the previous six-coordinate nitrosyl complexes. However, care must be used in examining the nonbonded interactions of the three NO orientations. The nonbonded interactions at this position arise from interaction with a 1-methylimidazole solvate molecule. There are no severe nonbonded interactions when the chloroform molecule is present. This is shown in both the svdWro plot Figure S6 and in the potential energy plot Figure 4f , where two distinct potentials have been plotted with the assumption of complete population by either imidazole or chloroform solvate molecules.

It is seen that population of the solvent site by chloroform does not lead to unfavorable nonbonded interactions with any of the observed positions of NO, whereas population by imidazole would allow population of only two NO sites. In the event, the occupancy of chloroform is sufficient Figures S12 to S17 of the Supporting information provide formal diagrams of the mean plane of the porphyrin cores for all derivatives studied at all temperatures.

Shown on each diagram are the orientations of both the imidazole and nitrosyl ligands with respect to the porphyrin core. There is thus some tendency towards the NO and imidazole ligands to have an approximately coplanar arrangement. The least-squares-determined populations for the NO oxygen sites in samples with two orientations see Table 1 can be used to determine thermodynamic parameters of the NO rotation.

The equilibrium constant, K, is calculated from the crystallographic populations of the NO orientations at the various temperatures. We make the assumption that all crystallographic measurements represent thermal equilibrium positions. The equilibrium constants, K, are calculated from the found NO orientation populations for the transition from the higher populated position to the lower populated position.

Although the two-state population assumption is probably not quite correct for these two systems, the calculations clearly agree with the conclusion that the relative NO orientations have small energy differences. Do these potential energy calculations have any applicability to biological systems? There are two known structures of NOMb and only a single orientation of NO has been reported for each.

Coordinates that are available from the Protein Data Bank, 1NPF 42 and 1HJT, 43 allow an approximate calculation of the potential energy as the oxygen atom is rotated and is given in Figure 8. This increased breadth appears to result from our inability to adequately include the contributions from the hydrogen atoms of the amino acids in the ligand binding pocket. As shown in the inset of Figure 8 , the protein has a much more tightly defined ligand binding volume than in the molecular crystals of the six-coordinate nitrosyls. The found NO oxygen position is indicated by a circle.

Density functional theory calculations were carried out on an isolated [Fe porphine NO 1-MeIm ] molecule to explore the energy costs of relative ligand orientations. Calculations were carried out to explore the overall energy as NO and imidazole were allowed to take on various orientations with respect to the porphyrin core. For all calculations either the 1-methylimidazole was placed in a position bisecting a meso-carbon and the NO was rotated or the NO was placed in a position bisecting a meso-carbon and the 1-methylimidazole was rotated.

An energy minimized structure was calculated for each axial ligand orientation. Because of the many calculations required in the study, the simplified porphine system [Fe porphine NO 1-MeIm ] was employed. The initial molecular configuration chosen had the FeNO and 1-MeIm planes coplanar and pointing toward a meso -carbon atom. The NO and 1-MeIm ligands were held fixed for each rotation; all other parameters were refined freely. Energy minima are observed when the two ligands are coplanar or orthogonal with a 0. In their calculation, the largest energy difference for all orientations is 2.

The core conformation of the three energy minimized structures are very similar. The new [Fe Porphine NO 1-MeIm ] calculations suggest an additional subtle effect of relative axial ligand orientation on the bonding parameters at iron. Please fill in a complete birthday Enter a valid birthday. Skin care Face Body. What happens when I have an item in my cart but it is less than the eligibility threshold? Should I pay a subscription fee to always have free shipping? No, you will enjoy unlimited free shipping whenever you meet the above order value threshold.

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