Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water

Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.     

Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase

Heme catalases prevent cells from oxidative damage by decomposing hydrogen peroxide into water and molecular oxygen. Here we investigate the factors that give rise to an undesirable side reaction competing with normal catalase activity, the migration of a radical from the heme active site to the protein in the principal reaction intermediate compound I (Cpd I). Recently, it has been proposed that this electron transfer reaction takes place in Cpd I of Helicobacter pylori catalase (HPC), but not in Cpd I of Penicillium vitale catalase (PVC), where the oxidation equivalent remains located on the heme active site. Unraveling the factors determining the different radical locations could help engineer enzymes with enhanced catalase activity for detection or removal of hydrogen peroxide. Using quantum mechanics/molecular mechanics metadynamics simulations, we show that radical migration in HPC is facilitated by the large driving force (-0.65 eV) of the subsequent proton transfer from a histidine residue to the ferryl oxygen atom of reduced Cpd I. The corresponding free energy in PVC is significantly smaller (-0.19 eV) and, as we argue, not sufficiently high to support radical migration. Our results suggest that the energetics of oxoferryl protonation is a key factor regulating radical migration in catalases and possibly also in hydroperoxidases.     

Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO.

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.     

The effect of point mutation on the equilibrium structural fluctuations of ferric Myoglobin

The ultrafast equilibrium fluctuations of the Fe(III)-NO complex of a single point mutation of Myoglobin (H64Q) have been studied using Fourier Transform 2D-IR spectroscopy. Comparison with data from wild type Myoglobin (wt-Mb) shows the presence of two conformational substates of the mutant haem pocket where only one exists in the wild type form. One of the substates of the mutant exhibits an almost identical NO stretching frequency and spectral diffusion dynamics to wt-Mb while the other is distinctly different in both respects. The remarkably contrasting dynamics are largely attributable to interactions between the NO ligand and a nearby distal side chain which provides a basis for understanding the roles of these side chains in other ferric haem proteins.     

时间分辨傅立叶变换红外发射光谱技术研究叔丁基亚硝酸酯的光解动力学

利用时间分辨傅立叶变换红外(TR-FTIR)发射光谱技术对叔丁基亚硝酸酯355 nm激光光解动力学进行研究. 通过对实验观测到的光解产物NO的时间分辨红外发射谱进行分析, 获得了NO的转动温度和相对振动布居, 并发现了振动布居的反转现象. 结合前人的工作, 我们确认了光解产物NO的最大振动布居量子数υ与光解光激发的母体分子N=O伸缩振动的泛频跃迁所涉及的振动量子数υ*之间的关系为υ=υ*-1.     

Infrared-infrared double resonance spectroscopy of cyanoacetylene in helium nanodroplets

Infrared-infrared double resonance spectroscopy is used as a probe of the vibrational dynamics of cyanoacetylene in helium droplets. The nu1 C-H stretching vibration of cyanoacetylene is excited by an infrared laser and subsequent vibrational relaxation results in the evaporation of approximately 660 helium atoms from the droplet. A second probe laser is then used to excite the same C-H stretching vibration downstream of the pump, corresponding to a time delay of approximately 175 micros. The hole burned by the pump laser is narrower than the single resonance spectrum, owing to the fact that the latter is inhomogeneously broadened by the droplet size distribution. The line width of the hole is characteristic of another broadening source that depends strongly on droplet size.     

Synthese und Eigenschaften von (Acido)(nitrosyl)phthalocyaninato(2–)ruthenium

Synthesis and Properties of (Acido)(nitrosyl)phthalocyaninato(2–)ruthenium (Acido)(nitrosyl)phthalocyaninato(2–)ruthenium, [Ru(X)(NO)pc^2–] (X = F, Cl, Br, I, CN, NCO, NCS, NCSe, N₃, NO₂) is obtained by acidification of a solution of bis(tetra(n-butyl)ammonium) bis(nitro)phthalocyaninato(2–)ruthenate(II) in tetrahydrofurane with the corresponding conc. mineral acid or aqueous ammonium salt solution. The nitrite-nitrosyl conversion is reversal in basic media. The cyclic and differential pulse voltammograms show mainly three quasi-reversible one-electron processes at 1.05, –0.65 and –1.25 V, ascribed to the first ring oxidation and the stepwise reduction to the complexes of type {RuNO}⁷ and {RuNO}⁸, respectively. The B < Q < N regions in the electronic absorption spectra are still typical for the pc^2– ligand, but are each split into two strong absorptions (14500/16500(B); 28000/30500(Q); 34500/37000 cm^–1(N)), whose relative intensities strongly depend on the nature of the axial ligand X. In the IR spectra is active the N–O stretching vibration between 1827 (X = I) and 1856 cm^–1 (F), the C–N stretching vibration at 2178 (X = NCO), 2072 (NCS), 2066 (NCSe), 2093 cm^–1 (CN), the N–N stretching vibration of the azide ligand at 2045 cm^–1, the fundamentals of the nitrito(O) ligand at 1501, 932, and 804 cm^–1, and the Ru–X stretching vibration at 483 (F), 332 (Cl), 225 (Br), 183 (I), 395 (N₃), 364 (ONO), 403 (CN), 263 (NCS), and 231 cm^–1 (NCSe). In the resonance Raman spectra, excited in coincidence with the B region, the Ru–NO stretching vibration and the very intense Ru–N–O deformation vibration are selectively enhanced between 580 and 618 cm^–1, and between 556 and 585 cm^–1, respectively.     

The Hydrated Excess Proton in the Zundel Cation H5O2+: The Role of Ultrafast Solvent Fluctuations

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H₅O₂⁺ prepared in room‐temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump‐probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H⁺ transfer vibration and its combination and overtones. Vibrational lifetimes of H₅O₂⁺ are found to be in the sub‐100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low‐frequency modes continuously modify the proton binding site while affecting its motions.     

QM/MM vibrational mode tracking

Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of biomolecules. When small subsystems of large molecules such as active centers of enzymes are studied, quantum chemical calculations based on quantum mechanics/molecular mechanics (QM/MM) coupling schemes are a valuable means to interpret the spectra. The goal of this work is a methodological pilot study on how to selectively and thus efficiently extract certain vibrational information for extended molecular systems described by QM/MM methods. This is achieved by an extension of the mode tracking algorithm and a comparison with the partial Hessian diagonalization approach. After validating the methodology for the CO stretching vibration of 2-butanone and a delocalized CO stretch in acetylacetone, the stretching and bending modes of the CO ligand in CO myoglobin are tracked. Such systems represent an ideal application for mode tracking, because only a few strongly localized vibrations are sought for, while the large remainder of the molecule is of interest only as far as it affects these local vibrations. This influence is treated exactly by mode tracking.     

The effects of collision energy, vibrational mode, and vibrational angular momentum on energy transfer and dissociation in NO2+-rare gas collisions: an experimental and trajectory study

A combined experimental and trajectory study of vibrationally state-selected NO2+ collisions with Ne, Ar, Kr, and Xe is presented. Ne, Ar, and Kr are similar in that only dissociation to the excited singlet oxygen channel is observed; however, the appearance energies vary by approximately 4 eV between the three rare gases, and the variation is nonmonotonic in rare gas mass. Xe behaves quite differently, allowing efficient access to the ground triplet state dissociation channel. For all four rare gases there are strong effects of NO2+ vibrational excitation that extend over the entire collision energy range, implying that vibration influences the efficiency of collision to internal energy conversion. Bending excitation is more efficient than stretching; however, bending angular momentum partially counters the enhancement. Direct dynamics trajectories for NO2+ + Kr reproduce both the collision energy and vibrational state effects observed experimentally and reveal that intracomplex charge transfer is critical for the efficient energy transfer needed to drive dissociation. The strong vibrational effects can be rationalized in terms of bending, and to a lesser extent, stretching distortion enhancing transition to the Kr+ -NO2 charge state.     

Spectroscopic and computational studies of nitrile hydratase: insights into geometric and electronic structure and the mechanism of amide synthesis

Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) Fe^III center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO₂^–), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS Fe^III and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.     

Direct Vibrational Energy Transfer in Monomeric Water Probed with Ultrafast Two Dimensional Infrared Spectroscopy

Vibrational relaxation dynamics of monomeric water molecule dissolved in d-chloroform solution were revisited using the two dimensional Infrared (2D IR) spectroscopy. The vibrational lifetime of OH bending in monomeric water shows a bi-exponential decay. The fast component (T₁=(1.2±0.1) ps) is caused by the rapid population equilibration between the vibrational modes of the monomeric water molecule. The slow component (T₂=(26.4±0.2) ps) is mainly caused by the vibrational population decay of OH bending mode. The reorientation of the OH bending in monomeric water is determined with a time constant of τ=(1.2±0.1) ps which is much faster than the rotational dynamics of water molecules in the bulk solution. Furthermore, we are able to reveal the direct vibrational energy transfer from OH stretching to OH bending in monomeric water dissolved in d-chloroform for the first time. The vibrational coupling and relative orientation of transition dipole moment between OH bending and stretching that effect their intra-molecular vibrational energy transfer rates are discussed in detail.     

3D Motions of Iron in Six‐Coordinate {FeNO}7 Hemes by Nuclear Resonance Vibration Spectroscopy

The vibrational spectrum of a six‐coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1‐MeIm)(NO)] (TpFPP=tetra‐para‐fluorophenylporphyrin; 1‐MeIm=1‐methylimidazole), has been studied by oriented single‐crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in‐plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in‐plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in‐plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out‐of‐plane Fe‐N‐O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v₅₀ as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe‐X‐O (X=N, C, and O) complexes is correlated with the Fe?XO bond lengths. The nature of highest frequency band at ≈560 cm^?1 has also been examined in two additional new derivatives. Previously assigned as the Fe?NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

Oxygen diffusion pathways in a cofactor-independent dioxygenase

Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O₂ diffusion is emerging, where specific channels guide O₂ to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O₂ reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O₂ at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O₂ in the absence of cofactors or metals, the way O₂ reaches the active site is similar to that reported for other O₂-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O₂ access that are conserved among very different types of proteins.     

Ultrafast energy migration pathways in self-assembled phospholipids interacting with confined water

Phospholipids self-assembled into reverse micelles in benzene are introduced as a new model system to study elementary processes relevant for energy transport in hydrated biological membranes. Femtosecond vibrational spectroscopy gives insight into the dynamics of the antisymmetric phosphate stretching vibration ν(AS)(PO(2))(-), a sensitive probe of local phosphate-water interactions and energy transport. The decay of the ν(AS)(PO(2))(-) mode with a 300-fs lifetime transfers excess energy to a subgroup of phospholipid low-frequency modes, followed by redistribution among phospholipid vibrations within a few picoseconds. The latter relaxation is accelerated by adding a confined water pool, an efficient heat sink in which the excess energy induces weakening or breaking of water-water and water-phospholipid hydrogen bonds. In parallel to vibrational relaxation, resonant energy transfer between ν(AS)(PO(2))(-) oscillators delocalizes the initial excitation.     

Effect of a charge relay on the vibrational frequencies of carbonmonoxy iron porphine adducts: the coupling of changes in axial ligand bond strength and porphine core size.

The effect of a charge relay involving Asp-His-Fe in peroxidase enzymes is explored using density functional theory (DFT) calculations of vibrational spectra and potential energy surfaces of carbonmonoxy model systems. The series of models consists of a carbonmonoxy iron porphine molecule with a trans imidazole ligand hydrogen-bonded to six different partners at the Ndelta position. Calculations on the oxy system and on models of the Asp-His-Ser catalytic triad of serine proteases were also performed to obtain an understanding of how the redistribution of charge in these systems may contribute to enzymatic function. The goal of the study is to relate the experimental frequencies in resonance Raman and Fourier transform infrared studies to bonding that is important for the function of heme enzymes. Calculations of both axial and in-plane modes exhibit trends that agree with experimental data. Comparisons of the charge distribution on the different models show that polarization of iron carbonomonoxy bonds consistent with the mechanism for peroxidase function leads to a frequency reduction in the C-O stretching mode nuCO. The combination of axial trans sigma-bonding and pi-bonding effects that include expansion of the porphine core result in little change in the Fe-C stretching frequency nuFe-CO in the series of molecules studied with different Ndelta-H hydrogen bonding. A particular role for the core size is discussed that demonstrates the applicability of trends observed in vibrational spectroscopy of hemes to the charge relay mechanism and other axial ligation effects. The bonding interactions described account for the increase in electron density on bound diatomic ligands, which is required for peroxidase function.