Nitric Oxide Dynamics in Truncated Hemoglobin: Docking Sites, Migration Pathways, and Vibrational Spectroscopy from Molecular Dynamics Simulations

Atomistic simulations of nitric oxide (NO) dynamics and migration in the trHbN of Mycobacterium tuberculosis are reported. From extensive molecular dynamics simulations (48 ns in total), the structural and energetic properties of the ligand docking sites in the protein have been characterized and a connectivity network between the ligand docking sites has been built. Several novel migration and exit pathways are found and are analyzed in detail. The interplay between a hydrogen-bonding network involving residues Tyr³³ and Gln⁵⁸ and the bound O₂ ligand is discussed and the role of Phe⁶² residue in ligand migration is examined. It is found that Phe⁶² is directly involved in controlling ligand migration. This is reminiscent of His⁶⁴ in myoglobin, which also plays a central role in CO migration pathways. Finally, infrared spectra of the NO molecule in different ligand docking sites of the protein are calculated. The pocket-specific spectra are typically blue-shifted by 5-10 cm⁻¹, which should be detectable in future spectroscopic experiments.     

Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane

The interactions of nitric oxide (NO) and organic nitroso compounds with heme proteins are biologically important, and adduct formation between NO-containing compounds and myoglobin (Mb) have served as prototypical systems for studies of these interactions. We have prepared crystals of horse heart (hh) MbNO from nitrosylation of aqua-metMb crystals, and we have determined the crystal structure of hh MbNO at a resolution of 1.9 A. The Fe-N-O angle of 147 degrees in hh MbNO is larger than the corresponding 112 degrees angle previously determined from the crystal structure of sperm whale MbNO (Brucker et al., Proteins 1998;30:352-356) but is similar to the 150 degrees angle determined from a MS XAFS study of a frozen solution of hh MbNO (Rich et al., J Am Chem Soc 1998;120:10827-10836). The Fe-N(O) bond length of 2.0 A (this work) is longer than the 1.75 A distance determined from the XAFS study and suggests distal pocket influences on FeNO geometry. The nitrosyl N atom is located 3.0 A from the imidazole N(epsilon) atom of the distal His64 residue, suggesting electrostatic stabilization of the FeNO moiety by His64. The crystal structure of the nitrosoethane adduct of ferrous hh Mb was determined at a resolution of 1.7 A. The nitroso O atom of the EtNO ligand is located 2.7 A from the imidazole N(epsilon) atom of His64, suggesting a hydrogen bond interaction between these groups. To the best of our knowledge, the crystal structure of hh Mb(EtNO) is the first such determination of a nitrosoalkane adduct of a heme protein.     

Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A,Mg2+ Ap5A,and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+

Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap₅A, Mn²⁺ Ap₅A, and Mg²⁺ Ap₅A have been determined by X-ray crystallography to resolutions of 1.6 Å, 1.85 Å, and 1.96 Å, respectively. The protein's lid domain is partially open, being both rotated and translated away from bound Ap₅A. The flexibility of the lid domain in the ternary state and its ability to transfer force directly to the the active site is discussed in light of our proposed entropic mechanism for catalytic turnover. The bound Zn²⁺ atom is demonstrably structural in nature, with no contacts other than its ligating cysteine residues within 5 Å. The B. stearothermophilus adenylate kinase lid appears to be a truncated zinc finger domain, lacking the DNA binding finger, which we have termed a zinc knuckle domain. In the Mg²⁺ Ap₅A and Mn²⁺ Ap₅A structures, Mg²⁺ and Mn²⁺ demonstrate six coordinate octahedral geometry. The interactions of the Mg²⁺-coordinated water molecules with the protein and Ap₅A phosphate chain demonstrate their involvement in catalyzing phosphate transfer. The protein selects for β-γ (preferred by Mg²⁺) rather than α-γ (preferred by Mn²⁺) metal ion coordination by forcing the ATP phosphate chain to have an extended conformation. Proteins 32:276–288, 1998. © 1998 Wiley-Liss, Inc.     

Structures of reduced and ligand‐bound nitric oxide reductase provide insights into functional differences in respiratory enzymes

Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N₂O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non‐heme Fe center. We report herein on the structures of the reduced and ligand‐bound forms of cytochrome c‐dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3–2.7 Å, to elucidate structure‐function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO‐bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH₃‐CH=N‐OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ～0.5 Å increase in the heme/non‐heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton‐pumping activity in cNOR, because redox‐coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non‐heme Fe distance even in the bulky ligand‐bound form of cNOR (～4.5 Å) than the heme/Cu distance in CCO (～5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N‐N coupling to produce a hyponitrite intermediate for the generation of N₂O. Proteins 2014; 82:1258–1271. © 2013 Wiley Periodicals, Inc.     

A theoretical study of myoglobin working as a nitric oxide scavenger

The mechanism for the reaction between nitric oxide (NO) and O₂ bound to the heme iron of myoglobin (Mb), including the following isomerization to nitrate, has been investigated using hybrid density functional theory (B3LYP). Myoglobin working as a NO scavenger could be of importance, since NO reversibly inhibits the terminal enzyme in the respiration chain, cytochrome c oxidase. The concentration of NO in the cell will thus affect the respiration and thereby the synthesis of ATP. The calculations show that the reaction between NO and the heme-bound O₂ gives a peroxynitrite intermediate whose O–O bond undergoes a homolytic cleavage, forming a NO₂ radical and myoglobin in the oxo-ferryl state. The NO₂ radical then recombines with the oxo-ferryl, forming heme-bound nitrate. Nine different models have been used in the present study to examine the effect on the reaction both by the presence and the protonation state of the distal His64, and by the surroundings of the proximal His93. The barriers going from the oxy-Mb and nitric oxide reactant to the peroxynitrite intermediate and further to the oxo-ferryl and NO₂ radical are around 10 and 7 kcal/mol, respectively. Forming the product, nitrate bound to the heme iron has a barrier of less than ~7 kcal/mol. The overall reaction going from a free nitric oxide and oxy-Mb to the heme bound nitrate is exergonic by more than 30 kcal/mol.     

Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling

Rational design of functional enzymes is a powerful strategy to gain deep insights into more complex native enzymes, such as nitric oxide reductase (NOR). Recently, we engineered a functional model of NOR by creating a two His and one Glu (2‐His‐1‐Glu) non‐heme iron center in sperm whale myoglobin (swMb L29E, F43H, H64, called Fe_BMb(‐His)). It was found that Fe_BMb(‐His) adopts a low‐spin state with bis‐His coordination in the absence of metal ions binding to the designed metal center. However, no structural information was available for the variant in this special spin state. We herein performed molecular modeling of Fe_BMb(‐His) and compared with the X‐ray structure of its copper bound derivative, Cu(II)‐CN^?‐Fe_BMb(‐His), resolved recently at a high resolution (1.65 Å) (PDB entry 3MN0). The simulated structure shows that mutation of Leu to Glu at position 29 in the hydrophobic heme pocket alters the folding behavior of Mb. The hydrogen bond between Glu29 and His64 further plays a role in stabilizing the bis‐His (His64/His93) coordination structure. This study offers an excellent example of using molecular modeling to gain insights in rational design of both structural and functional proteins. Proteins 2011. © 2010 Wiley‐Liss, Inc.     

Structural Assignment of Spectra by Characterization of Conformational Substates in Bound MbCO

Residue motions of the distal heme pocket and bound CO ligand of carbonmonoxy Myoglobin are studied using a combination of molecular dynamics simulations and quantum chemical methods. Using mixed quantum mechanics/molecular mechanics calculations together with sampling from molecular dynamics simulations (QM/MM(MD)), the experimentally observed spectroscopic A₀ and A₁ substates of the bound CO ligand are assigned to the open and closed conformation of His⁶⁴ and the His_ɛ⁶⁴ tautomer, respectively. Several previously proposed origins of the A₃ substate, including rotamers of the doubly protonated His⁶⁴H⁺ side chain, His⁶⁴H⁺ inside the distal pocket, and cooperative motions with Arg⁴⁵, are investigated with QM/MM(MD). However, the signatures of the calculated infrared spectra do not agree with the experimentally observed ones. For additional insight on this, extensive molecular dynamics simulations are used together with improved electrostatics for the bound ligand. A CO fluctuating charge model is developed to describe the ab initio dipole and quadrupole moments of the bound ligand. CO absorption spectra are then obtained directly from the dynamics simulations. Finally, the electrostatics of the heme pocket is examined in detail in an attempt to determine the structural origins of the observed spectroscopic A-states from MD simulations. However, contrary to related simulations for unbound CO in myoglobin, the shifts and splittings for carbonmonoxy Myoglobin are generally small and difficult to relate to structural change. This suggests that coupling of the CO motion to other degrees of freedom, such as the Fe-CO stretching and bending, is important to correctly describe the dynamics of bound CO in myoglobin.     

Binding of VIVO2+ to the Fe binding sites of human serum transferrin. A theoretical study

The binding of V^IVO²⁺ to human serum transferrin (hTF) at the Fe^III binding sites is addressed. Geometry optimization calculations were performed for the binding of V^IVO²⁺ to the N-terminal lobe of hTF (hTF_N), and indicate that in the presence of CO₃ ^2? or HCO₃ ^?, V^IV is bound to five atoms in a distorted geometry. The structures of V^IVO–hTF_N species optimized at the semiempirical level were also used to calculate the ⁵¹V and ¹⁴N A tensors by density functional theory methods, and were compared with the reported experimental values. Globally, of all the calculated V^IVO–hTF structures, the one that yields the lowest calculated heats of formation and minimum deviations from the experimental values of the ⁵¹V and ¹⁴N A tensor components is the structure that includes CO₃ ^2? as a synergistic anion. In this structure the V=O bond length is approximately 1.6 Å, and the vanadium atom is also coordinated to the phenolate oxygen atom of Tyr188 (at approximately 1.9 Å), the aspartate oxygen atom of Asp63 (at approximately 1.9 Å), the His249 Nτ atom (at approximately 2.1 Å), and a carbonate oxygen atom (at approximately 1.8 Å). The Tyr95 phenolic ocygen atom is approximately 3.3 Å from the metal center, and thus is very weakly bound to V^IV. All of these oxygen atoms are able to establish dipolar interactions with groups of the protein.     

Monomeric molybdenum(V) complexes. 4. The structure of tetraphenylarsonium oxodichloro(N-2-oxophenylsalicylideniminato)molybdate(V), [Ph4As] [MoOCl2(SalphO)]

The structure of [Ph₄As] [MoOCl₂(SalphO)], where SalphO is N-2-oxophenylsalicylideniminate dianion, has been determined by X-ray crystallography. The complex crystallizes in the monoclinic space group P2₁/n with a = 11.829(2), b = 16.149(3), c = 17.410(3) Å, β = 97.485(15)° and Z = 4. The calculated and observed densities and 1.566 and 1.573(10) g cm^?3, respectively. Block-diagonal least-squares refinement of the structure using 4722 independent reflections with I ? 3σ(I) converged at R = 0.0345 and R_w = 0.0484. The crystal contains [Ph₄As]⁺ cations and [MoOCl₂(SalphO)]^? anions. The Mo atom in the anion is in a distorted octahedral coordination environment. A planar terdentate Schiff base ligand occupies meridional positions with the N atom trans to the terminal oxo group (O_t). Two Cl atoms are cis to the O_t atom. The Mo atom is displaced by 0.33 Å from the equatorial plane toward the O_t atom. The MoO_t distance is 1.673(3) Å. The MoN bond trans to the O_t atom is 2.298(4) Å. The two MoCl bond lengths are 2.371(1) and 2.408(1) Å. The difference of 0.037 Å is significant (30 σ). Preparations of the title complex and the related complexes are also described.     

Structure of erythrocruorin in different ligand states refined at 1.4 A resolution.

The crystal structure of erythrocruorin has been refined by constrained crystallographic refinement at 1·4 Å resolution in the following ligand states: aquomet (Fe³⁺, high spin), cyanomet (Fe³⁺, low spin), deoxy (Fe²⁺, high spin) and carbonmonoxy (Fe²⁺, low spin). The final R-value at this resolution is better than 0·19 for each of these models. The positional errors of the co-ordinates are less than 0·1 Å.The root-mean-square differences between the deoxygenated and the ligated erythrocruorin are about 0·1 Å, being largest for cyanomet-erythrocruorin. The changes in tertiary structures propagate from the location of primary events and often fade out at the molecular surface. Helix E passing the distal side of the haem group is affected most by the direct contact with the ligand bound to the haem iron.Steric hindrance by the distal residue IleE11 forces the cyanide and carbonmonoxide ligands to bind at an angle to the haem axis. The strain at the ligand is partially relieved by movement of the haem deeper into the haem pocket and rearrangement of neighbouring residues.The differences in iron location with respect to the mean haem plane are spin-dependent but unexpectedly small (the largest value is 0·15 Å between deoxy and carbonmonoxy-erythrocruorin). Spin state changes seem to have little influence on the porphyrin stereochemistry; it is determined primarily by the chemical properties of the ligand and its interaction with the haem and the globin. These non-covalent interactions are largely responsible for the initiation of the structural changes on ligand binding.     

On the mechanism of action of thiamin enzymes, Crystal structure of 2-(α-hydroxyethyl)thiamin pyrophosphate (HETPP). Complexes of HETPP with zinc(II) and cadmium(II)

The crystal structure of the 2-(α-hydroxethyl) thiamin pyrophosphate (LH₂) was solved by X-ray diffraction. Crystallographic data: space group F2dd, a=7.922(4) Å, b=33.11(2) Å, c=36.232(10) Å, V=9503(9) ų, z=16. Metal complexes of the general formula K₂{[M(LH)Cl₂]₂} (M=Zn²⁺, Cd²⁺) were isolated from methanolic solutions and characterized by elemental analysis, IR, Raman, and ¹³C CP MAS NMR spectra. They were also characterized by ¹³C NMR, ³¹P NMR, ¹¹³Cd NMR, ES-MS, and ¹H NMR ROESY spectra in D₂O solutions. The data provide evidence for the bonding of the metals to the N(1′) atom of the pyrimidine ring and to the pyrophosphate group. The free ligand and the metal-coordinated ligand adopt the S conformation. Since thiamin cofactor, substrate, and metal ions are present in our system, the extracted results directly refer to thiamin catalysis and possible functional implications are correlated and discussed.     

Preparation,properties and crystal structures of nickel(II) complexes with acyclic schiff bases derived from 2,6-diformyl-4-chlorophenol and 1,5-diamino-3-thiapentane or 3,3′-diamino-N-methyl-dipropylamine

Nickel(II) complexes with the compartmental Schiff bases derived from 2,6-diformyl-4-chlorophenol and 1,5-diamino-3-thiapentane (H₂L¹) or 3,3′-diamino-N-methyl-dipropylamine (H₂L²) were synthesized, and the crystal structures of [Ni(L¹)- (py)₂] and [Ni(L²)(dmf)]·H₂0 were determined by X-ray crystallography.Ni(L¹)(py)₂ is monoclinic, space group C2/c, with a= 18.457(6), b = 11.116(7), c= 16.098(6) Å, and β = 115.79(5)°; D_c = 1.49 g cm⁻³ for Z = 4. The structure was refined to the final R of 6.9%. The molecule has C₂ symmetry. The nickel atom is six-coordinated octahedral. Selected bond lengths are: NiO 2.04(1) Å, NiN (L¹) 2.08(1) Å, NiN(py) 2.17(1) Å.[Ni(L²)(dmf)]·H₂O is monoclinic, space group P2₁/n, with a = 17.329(6), b = 13.322(7), c = 12.476(7) Å and β = 95.43(5)°; D_c = 1.45 g cm⁻³ for Z = 4. The structure was refined to the final R of 5.1%. The nickel atom is bonded in the octahedral geometry to the bianionic pentadentate ligand L² and to one molecule of dimethylformamide. Selected bond lengths are: NiO (charged) 2.063(3) Å (mean value), NiO (neutral) 2.120(3) Å, NiN (planar) 2.050(3) Å (mean value), NiN (tetrahedral) 2.177(3) Å.     

An energy transfer equilibrium between two identical copies of a ribosome-bound fluorescent transfer RNA analogue: implications for the possible structure of codon-anticodon complexes.

When yeast tRNA_Pf^Phe, a derivative of tRNA^Phe in which proflavine replaces the Y base, is bound simultaneously to both the peptidyl and aminoacyl sites of a 70 S Escherichia coli ribosome, there is a rapid mutual energy transfer between the two bound tRNAs. Analysis of this energy transfer yields an upper limit for the proflavine-proflavine distance of 20 Å. It also allows an unequivocal measurement of the emission spectrum of tRNA_Pf^Phe bound at the aminoacyl site. In the presence of message this spectrum is very different from that seen in the peptidyl site, implying that in the two sites the hypermodified bases exist in significantly different environments. The rapid energy transfer leads to some loss of fluorescence anisotropy. This can be analyzed to obtain an estimate of the angle between the two proflavines: 28 ° ± 10 ° or 152 ° ± 10 °. Taken together all of these results place severe constraints on possible models of codon-anticodon complexes. The mutual energy transfer seen and analyzed on the ribosome is a convenient aspect of fluorescence spectroscopy, and it is one that should see broad application where multiple copies of a fluorescent ligand interact on a macromolecular substrate.     

Crystal structures of the nitrite and nitric oxide complexes of horse heart myoglobin

Nitrite is an important species in the global nitrogen cycle, and the nitrite reductase enzymes convert nitrite to nitric oxide (NO). Recently, it has been shown that hemoglobin and myoglobin catalyze the reduction of nitrite to NO under hypoxic conditions. We have determined the 1.20 A resolution crystal structure of the nitrite adduct of ferric horse heart myoglobin (hh Mb). The ligand is bound to iron in the nitrito form, and the complex is formulated as MbIII(ONO-). The Fe-ONO bond length is 1.94 A, and the O-N-O angle is 113 degrees . In addition, the nitrite ligand is stabilized by hydrogen bonding with the distal His64 residue. We have also determined the 1.30 A resolution crystal structures of hh MbIINO. When hh MbIINO is prepared from the reaction of metMbIII with nitrite/dithionite, the FeNO angle is 144 degrees with a Fe-NO bond length of 1.87 A. However, when prepared from the reaction of NO with reduced MbII, the FeNO angle is 120 degrees with a Fe-NO bond length of 2.13 A. This difference in FeNO conformations as a function of preparative method is reproducible, and suggests a role of the distal pocket in hh MbIINO in stabilizing local FeNO conformational minima.     

Synthesis and characterization of technetium(V) complexes with tridentate schiff base ligands. X-ray crystal structure of chloro[N-(2-hydroxyphenyl)salicylideneiminato]oxotechnetium(V)

Five-coordinate technetium(V) complexes of the form TcO(L)Cl where L is one of the two tridentate Schiff base ligands N-(2-oxidophenyl)salicylideneiminate or N-(2-mercaptophenyl)salicylideneiminate have been synthesized and characterized. These neutral complexes precipitate from methanol upon reaction of the Schiff base ligand with TcOCl₄^?. A single crystal X-ray structure determination shows that the chloro [[N-(2-oxidophenyl)salicylideneiminato](2?)-N,O,O′]oxotechnetium(V) complex, [TcO(C₁₃H₉NO₂)Cl], formula weight 362, has a distorted square pyramidal coordination geometry with the oxo ligand in the axial position. The steric requirements of the oxo group cause the Tc atom to be displayed 0.67 Å out of the mean equatorial plane of the other four donor atoms. This complex crystallizes in the monoclinic space group P2₁/a with a = 13.423(6) Å, b = 12.570(5) Å, c = 7.769(3) Å, β = 106.53(5)°, V = 1256.7(9) ų, and Z = 4. The structure has been refined to R = 0.047 for 1775 observed reflections.     

The crystal and molecular structure of bis(2,2′-dipyridylamine-N,N′)di(nitrato-O)cadmium(II); Solid state 113Cd NMR,components and orientation of the chemical shift tensor relative to the donor ligands

The structure of the titled compound has been determined and refined. The structure consists of isolated molecules separated by ordinary Van der Waals' distances. The Cd atom is on a crystallographic center of symmetry. The coordination polyhedron of the Cd atom is distorted octahedral with four pyridine nitrogen donors in the equatorial plane and with axial oxygen atoms from the nitrate groups. The CdO distance is 2.599(4) Å, the CdN distances are 2.310(4) and 2.316(3) Å, and the NCdN bite angle is 79.0(1)°. The solid state magic angle spinning/cross polarization ¹¹³Cd NMR isotropic chemical shift is +51.4 ppm and the components of the chemical shift tensor are: S₁₁= −92 ppm, S₃₃ = +208 ppm and S₂₂ = +39 ppm and their directions are: in the CdN₄ plane and bisecting the NCdN bite angle, perpendicular to the CdN₄ plane and the third perpendicular to the other two, respectively. This permits the assignment of contributions to the chemical shift tensor of 50 ppm from pyridine nitrogen and of −50 ppm from nitrate oxygen. From the tensor components, atomic nitrogen can be distinguished from aliphatic nitrogen donors. Crystal data: C₂₀H₁₈O₆N₈Cd; M_r = 578.8, F(000) = 580, monoclinic, P2₁/c, a = 8.591(1), b = 16.496(2), c = 7.878(1) Å, β = 95.97°, λ = 0.71073 Å, Mo Kα, V = 1110(1) ų. Z = 2, D_m = 1.73(2), D_x = 1.73 g/cm³, μ = 10.3 cm⁻¹, R_f = 0.039, 1834 reflections, 160 parameters, T ∼ 298 K. Refinement was by full matrix least-squares with anisotropic temperature factors.     

Crystal and molecular structure of the (2,2′-diaminobiphenyl)(R,R-trans-1,2-diaminocyclohexane)platinum(II) complex

2,2′-Diaminobiphenyl-R,R-trans-1,2-diaminocyclohexaneplatinum(II) Chloride Trihydrate, (R,R-chxn)(dabp)Pt]Cl₂·3H₂O, crystallizes in the space group _p2₁2₁2₁ (D₂⁴, No. 19) with a = 6.219(4) Å, b = 17.633(2) Å, c = 21.523(3) Å, V = 2,360.4(8) ų, ?_calcd = 1.739 g cm^?3, ?_measd = 1.74 g cm^?3, and Z = 4. Diffraction data were collected with a Picker FACS-1 four-circle diffractometer. The structure was solved by the heavy atom method and refined by least-square calculations to residuals R = 0.0586 and weighted R = 0.0668. The 2,2′-diaminobiphenyl ligand exhibits complete stereospecificity in its coordination to platinum(II) ion with λ chiral conformation.     

Synthesis of heterodinuclear FeRu(CO)6(R-DAB(6e))(R-DABRNC(H)C(H)NR) Part XV. Comparison of the reactivities of heterodinuclear FeRu(CO)6(R-DAB(6e)) and homodinuclear analogues M2(CO)6(R-DAB(6e)) (M = Fe,Ru). Single-crystal x-ray structures of FeRu(CO)6(i-Pr-DAB(6e)) and FeRu(CO)5(i-Pr-DAB(4e))(C3H4)

The reactions of Fe(CO)₃(R-DAB; R¹, H(4e)) (1a: R = i-Pr, R¹ = H; 1b: R = t-Bu, R¹ = H; 1c: R = c-Hex, R¹ = H; 1e: R = p-Tol, R¹ = H; 1f: R = i-Pr, R¹ = Me) with Ru₃(CO)₁₂ and of Ru(CO)₃(R-DAB; R¹, H(4e)) (2a: R = i-Pr, R¹ = H; 2d: R = CH(i-Pr)₂, R¹ = H) with Fe₂(CO)₉ in refluxing heptane both afforded FeRu(CO)₆(R-DAB; R¹, H(6e)) (3) in yields between 50 and 65%.The coordination mode of the ligand has been studied by a single crystal X-ray structure determination of FeRu(CO)₆(i-Pr-DAB(6e)) (3a). Crystals of 3a are monoclinic, space group P2₁/a, with four molecules in a unit cell of dimensions: a = 22.436(3), b = 8.136(3), c = 10.266(1) Å and β = 99.57(1)°. The structure was refined to R = 0.049 and R_w = 0.052 using 3045 reflections above the 2.5σ(I) level. The molecule contains an FeRu bond of 2.6602(9) Å, three terminally bonded carbonyls to Fe, three terminally bonded carbonyls to Ru and bridging 6e donating i-Pr-DAB ligand. The i-Pr-DAB ligand is coordinated to Ru via N(1) and N(2) occupying an apical and equatorial site respectively (RuN(1) = 2.138(4) RuN(2) = 2.102(3) Å). The C(2)N(2) moiety of the ligand is η²-coordinated to Fe with C(2) in an apical and N(2) in an equatorial site (FeC(2) = 2.070(5) and FeN(2) = 1.942(3) Å).The ¹H and ¹³C NMR data indicate that in all FeRu(CO)₆(R-DAB(6e)) complexes (3a to 3f) exclusively η²-CN coordination to the Fe atom and not to the Ru atom is present irrespective of whether 3 was prepared by reaction of Fe(CO)₃(R-DAB(4e)) (1) with Ru₃(CO)₁₂ or by reaction of Ru(CO)₃(R-DAB(4e)) (2) with Fe₂(CO)₉. In the case of FeRu(CO)₆(i-Pr-DAB; Me, H(6e)) (3f) the NMR data show that only the complex with the C(Me)N moiety of the ligand σ-N coordinated to the Ru atom and the C(H)N moiety η²-coordinated to the Fe atom was formed. Variable temperature NMR experiments up to 140 °C showed that the α-diimine ligand in 3a is stereochemically rigid bonded.FeRu(CO)₆(R-DAB(6e)) (3a and 3e) reacted with allene to give FeRu(CO)₅(R-DAB(4e))(C₃H₄) (4a and 4e). A single crystal X-ray structure determination of FeRu(CO)₅(i-Pr-DAB(4e))(C₃H₄) (4a) was performed. Crystals of 4a are triclinic, space group P1, with two molecules in a unit cell of dimensions: a = 9.7882(7), b = 12.2609(9), c = 8.3343(7) Å, α = 99.77(1)°, β = 91.47(1)° and γ = 86.00(1)°. The structure was refined to R = 0.028 and R_w = 0.043 using 4598 reflections above the 2σ(I) level. The molecule contains an FeRu bond of 2.7405(7) Å and three terminally bonded carbonyls to iron. Two carbonyls are terminally bonded to the Ru atom together with a chelating 4e donating i-Pr-DAB ligand [RuN = 2.110(1) (mean)]. The allene ligand is coordinated in an η³-allylic fashion to the Fe atom while the central carbon of the allene moiety is σ-bonded to the Ru atom (FeC(14) = 2.166(3), FeC(15) = 1.970(2), FeC(16) = 2.127(3) and RuC(15) = 2.075(2) Å). The ¹H and ¹³C NMR data show that in solution the coordination modes of the R-DAB and the allene ligands are the same as in the solid state.Thermolysis reactions of 3a with R-DAB or carbodiimides gave decomposition and did not afford C(imine)C(reactant) coupling products. Thermolysis reactions of 3a with M₃(CO)₁₂ (M = Ru, Os) and Me₃NO gave decomposition. When the reaction of 3a with Me₃NO was performed in the presence of dimethylacetylenedicarboxylate (DMADC) the known complex FeRu(CO)₄(i-Pr-DAB(8e))(DMADC) (5a) was formed in low yield. In 5a the R-DAB ligand is in the 8e coordination mode with both the imine bonds η²-coordinated to iron. The acetylene ligand is coordinated in a bridging fashion, parallel with the FeRu bond.     

The synthesis and structural characterization of (2-pyridyldiphenylphosphine oxide)platinum(IV)tetrabromide. A chelating phosphine oxide with a substantially bent PtOP angle

The complex (pyPh₂PO)PtBr₄ (pyPh₂PO is 2-pyridyldiphenylphosphine oxide) has been synthesized by three different pathways, and its structure has been established by X-ray crystallography. C₁₇H₁₄Br₄NOPPt crystallizes in the space group P2₁/c (no. 14) with cell dimensions (at 140 K) of a = 13.696(7), b= 16.653(5), c = 17.612(7) Å, β = 92.23(4)°, Z = 8 and V = 3993(3) ų. The structure was refined by block-cascade least-squares to a conventional R value of 0.048 using 3647 significant data. The structure involves a six-coordinate platinum((IV) ion with the chelated ligand bound through its nitrogen and oxygen atoms. The two crystallography independent molecules in the asymmetric unit have very similar dimensions. To our knowledge this is the first reported structure of a chelating phosphine oxide. The PtOP angles within the rings are 114.4(6)° and 117.4(6)°.     

Structure of nitric oxide hemoglobin

We have compared the structure of horse nitric oxide hemoglobin (HbNO) and methemoglobin in the oxy quaternary structure by difference Fourier analysis at 2.8 Å resolution. Both nitric oxide and oxygen assume bent co-ordination geometry and form low-spin complexes in binding to heme; on the basis of preferred ligand and heme stereochemistry, HbNO is the closest analog of HbO₂ (oxyhemoglobin) examined to date. To the resolution of the X-ray data, the stereochemistry of the heme-NO complex in hemoglobin and the corresponding free heme complex appears similar. In contrast, the ligand pockets in hemoglobin hinder binding of cyanide and carbon monoxide in their preferred linear axial co-ordination modes and force them to assume a strained off-axis binding stereochemistry. The structural similarity between HbNO and HbO₂ is reflected in their kinetic behavior, which is similar, and distinct from that of carboxyhemoglobin.