Stiffness, resilience, compressibility

Leu, Bogdan M.; Sage, J. Timothy

doi:10.1007/s10751-016-1275-8

Cited by 6 publications

(3 citation statements)

References 54 publications

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“…We noted previously that both stiffness and resilience should vary with orientation. 47 We also reported significant differences between axial and equatorial stiffnesses for imidazole and imidazolate complexes, 43 presumed to reflect differences in relative bond strength. However, Table 1 records the first stiffness values measured along independent directions in the porphyrin plane.…”

Section: ■ Results and Discussionmentioning

confidence: 74%

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?

et al. 2018

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Compared to well studied diatomic ligands (NO, CN, CO), the axial bonds of carbene hemes is much less known although its significance in biological chemistry. The unusually large quadrupole splitting (Δ E = +2.2 mm·s) and asymmetric parameter (η = 0.9) of the five-coordinate heme carbene [Fe(TTP)(CCl)], which is the largest among all known low spin ferrohemes, has driven investigations by means of Mössbauer effect Nuclear Resonance Vibrational Spectroscopy (NRVS). Three distinct measurements on one single crystal (two in-plane and one out-of-plane) have demonstrated comprehensive vibrational structures including stretch (429) and bending modes (472 cm) of the axial Fe-CCl, and revealed iron vibrational anisotropy in three orthogonal directions for the first time. Frontier orbital analysis especially comparisons with diatomic analogues (NO, CN, CO) suggest that CCl, similar to NO, has led to strong but anisotropic π bonding in a ligand-based "4C"-coordinate which induced the vibrational anisotropies and very large Mössbauer parameters. This is contrasted to CN and CO complexes which possess a porphyrin-based "4N"-coordinate electronic and vibrational structures due to inherent on-axis linear ligation.

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Section: ■ Results and Discussionmentioning

confidence: 74%

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?

et al. 2018

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“…4. There is an excess of low-frequency modes relative to experiment, 38,39 which might be related to the expansion of the protein at T = 300 K, at which simulations were performed, compared to the experimental temperature of T = 68 K. Table 1 shows the splitting of the variance of the force acting on the heme into electrostatic and van der Waals (vdW) components and, additionally, into the components from the water and protein parts of the thermal bath. Note that the components do not add to the total force variance because of cross-correlations.…”

Section: Resultsmentioning

confidence: 97%

“…The splitting into components indicates that vdW interactions and electrostatics contribute comparable magnitudes to the force variance. The softening of iron vibrations cannot therefore be fully 4 Experimental (Exp., 38,39 T = 68 K ) and simulation (Sim., T = 300 K) vibrational density of states for Cyt-Ox ( ν = ω/(2πc), c is the speed of light). Simulations were done for 1 ns in the NVE ensemble with non-rigid protons and 0.25 fs integration step (configurations saved every 1 fs).…”

Section: Resultsmentioning

confidence: 99%

Ergodicity breaking of iron displacement in heme proteins

Seyedi

Matyushov

2017

Soft Matter

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We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.

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Experimental calibration of the reduced partition function ratios of tetrahedrally coordinated silicon from the Debye–Waller factors

Zhang

Chen

Dera

et al. 2021

Contrib Mineral Petrol

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Stiffness, resilience, compressibility

Cited by 6 publications

References 54 publications

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?

Ergodicity breaking of iron displacement in heme proteins

Experimental calibration of the reduced partition function ratios of tetrahedrally coordinated silicon from the Debye–Waller factors

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Stiffness, resilience, compressibility

Cited by 6 publications

References 54 publications

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN–) Analogues in the Axial Bond?

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN–) Analogues in the Axial Bond?

Ergodicity breaking of iron displacement in heme proteins

Experimental calibration of the reduced partition function ratios of tetrahedrally coordinated silicon from the Debye–Waller factors

Contact Info

Product

Resources

About

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN^–) Analogues in the Axial Bond?