Resonance Raman studies of xanthine oxidase: The reduced enzyme-product complex with violapterin

A study of the molecular, electronic, and vibrational characteristics of the molybdenum-containing enzyme complex xanthine oxidase with violapterin has been carried out using density functional theory calculations and resonance Raman spectroscopy. The electronic structure calculations were carried out on a model consisting of the enzyme molybdopterin cofactor [in the four-valent, reduced state; Mo(IV)O(SH)] covalently linked to violapterin (1H,3H,8H-pteridine-2,4,7-trione in the neutral form) via an oxygen bridge, Mo-O-C7. Full geometry optimizations were performed for all models using the SDD basis set and the three-parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional. Harmonic vibrational frequencies were determined for a variety of isotopes in an attempt to correlate experimentally observed shifts upon 18O-labeling of the Mo-OR bridge to bound product as well as shifts seen upon substitution of solvent-exchangeable protons in samples prepared in D2O. The theoretical vibrational frequencies compared favorably with experimentally observed vibrational modes in the resonance Raman spectra of the reduced xanthine oxidase-violapterin complex prepared in H2O and D2O and with 18O-labeled product. Correlating the isotopic shifts from the calculations with those from the resonance Raman experiments resulted in complete normal mode assignments for all modes observed in the 350-1750 cm(-1) range. The present work demonstrates that a model in which the violapterin is coordinated to the molybdenum of the active site in a simple end-on manner via the hydroxyl group introduced by an enzyme accurately predicts the observed resonance Raman spectrum of the complex. Given the numerous modes involving the bridging oxygen, a side-on binding mode can be eliminated.     

Vibrational dynamics of ice in reverse micelles

The ultrafast vibrational dynamics of HDO:D(2)O ice at 180 K in anionic reverse micelles is studied by midinfrared femtosecond pump-probe spectroscopy. Solutions containing reverse micelles are cooled to low temperatures by a fast-freezing procedure. The heating dynamics of the micellar solutions is studied to characterize the micellar structure. Small reverse micelles with a water content up to approximately 150 water molecules contain an amorphous form of ice that shows remarkably different vibrational dynamics compared to bulk hexagonal ice. The micellar amorphous ice has a much longer vibrational lifetime than bulk hexagonal ice and micellar liquid water. The vibrational lifetime is observed to increase linearly from 0.7 to 4 ps with the resonance frequency ranging from 3100 to 3500 cm(-1). From the pump dependence of the vibrational relaxation the homogeneous linewidth of the amorphous ice is determined (55+/-5 cm(-1)).     

Probing the valence character of O 1s-->Rydberg excited O2 by participator Auger decay measurements and partial ion yield spectroscopy following x-ray absorption

The valence character of O 1s-->Rydberg excited O2 is investigated by means of participator Auger decay spectroscopy, performed at selected photon energies across the K-shell resonance region, and by means of partial ion yield x-ray absorption spectroscopy. For several of the excitation energies studied, the authors find substantial sigma*(4Sigmau-, 2Sigmau-) valence character being mixed with nssigma and npsigma (4Sigmau-, 2Sigmau-) Rydberg states. An experimental indication of a coupling between the channels associated with quartet and doublet ion cores is considered and discussed. New spectroscopic constants are derived for the singly ionized X 2Pig state of O2 based on the observation of at least 20 vibrational sublevels.     

Vibrational relaxation of the H2O bending mode in liquid water

We have studied the vibrational relaxation of the H(2)O bending mode in an H(2)O:HDO:D(2)O isotopic mixture using infrared pump-probe spectroscopy. The transient spectrum and its delay dependence reveal an anharmonic shift of 55+/-10 cm(-1) for the H(2)O bending mode, and a value of 400+/-30 fs for its vibrational lifetime.     

Infrared action spectroscopy and dissociation dynamics of the HOOO radical

The HOOO radical has long been postulated to be an important intermediate in atmospherically relevant reactions and was recently deemed a significant sink for OH radicals in the tropopause region. In the present experiments, HOOO radicals are generated in a pulsed supersonic expansion by the association of O(2) and photolytically generated OH radicals, and the spectral signature and vibrational predissociation dynamics are investigated via IR action spectroscopy, an IR-UV double resonance technique. Rotationally resolved IR action spectra are obtained for trans-HOOO in the fundamental (nu(OH)) and overtone (2nu(OH)) OH stretching regions at 3569.30 and 6974.18 cm(-1), respectively. The IR spectra exhibit homogeneous line broadening, characteristic of a approximately 26-ps lifetime, which is attributed to intramolecular vibrational redistribution and/or predissociation to OH and O2 products. In addition, an unstructured feature is observed in both the OH fundamental and overtone regions of HOOO, which is likely due to cis-HOOO. The nascent OH X(2)Pi, v = 0 or v = 1, products following vibrational predissociation of HOOO, nu(OH) or 2nu(OH), respectively, have been investigated using saturated laser-induced fluorescence measurements. A distinct preference for population of Pi(A') Lambda-doublets in OH was observed and is indicative of a planar dissociation of trans-HOOO in which the symmetry of the bonding orbital is maintained.     

N_2O分子C~1Ⅱ态的吸收光谱及解离动力学

通过四波混频差频的方法产生高分辨的真空紫外激光,用以测量143.6至146.9 nm范围内的射流冷却N_2O分子吸收光谱,对应于C~1Ⅱ←Ⅹ~1∑~+的吸收跃迁.谱图显示出三个分立的振动谱峰叠加在宽吸收背景上,谱峰间隔分别是521和482 cm~(-1).前人的高精度量子化学计算表明C~1Ⅱ态在N-O键长方向表现为无势垒的排斥态.而在N-N键伸缩及N_2O弯曲振动方向则表现为束缚态,因此观测到的振动谱峰被归属为激发态的Feshbach共振.通过反Fourier变换可以得到Feshbach共振对应的非稳定周期轨道的特征周期为61 fs,相应的振动频率为546 cm~(-1).鉴于这一频率与弯曲振动频率非常接近,非稳定周期轨道被认为是由C~1Ⅱ态的弯曲振动与解离运动相互作用而形成的,N-N伸缩振动没有参与形成非稳定周期轨道.由此,N_2O分子C~1Ⅱ态光激发-解离过程得以清晰地阐述.     

N_2O分子C~1Π态的吸收光谱及解离动力学

通过四波混频差频的方法产生高分辨的真空紫外激光,用以测量143.6至146.9 nm范围内的射流冷却N2O分子吸收光谱,对应于C1Π←X1Σ+的吸收跃迁.谱图显示出三个分立的振动谱峰叠加在宽吸收背景上,谱峰间隔分别是521和482 cm-1.前人的高精度量子化学计算表明C1Π态在N—O键长方向表现为无势垒的排斥态,而在N—N键伸缩及N2O弯曲振动方向则表现为束缚态,因此观测到的振动谱峰被归属为激发态的Feshbach共振.通过反Fourier变换可以得到Feshbach共振对应的非稳定周期轨道的特征周期为61 fs,相应的振动频率为546 cm-1.鉴于这一频率与弯曲振动频率非常接近,非稳定周期轨道被认为是由C1Π态的弯曲振动与解离运动相互作用而形成的,N—N伸缩振动没有参与形成非稳定周期轨道.由此,N2O分子C1Π态光激发-解离过程得以清晰地阐述.     

Hydrogen-bond dynamics and Fermi resonance in high-pressure methane filled ice

High-pressure, variable temperature infrared spectroscopy and first-principles calculations on the methane filled ice structure (MH-III) at high pressures are used to investigate the vibrational dynamics related to pressure induced modifications in hydrogen bonding. Infrared spectroscopy of isotopically dilute solutions of H(2)O in D(2)O is employed together with first-principles calculations to characterize proton dynamics with the pressure induced shortening of hydrogen bonds. A Fermi resonance is identified and shown to dominate the infrared spectrum in the pressure region between 10 and 30 GPa. Significant differences in the effects of the Fermi resonance observed between 10 and 300 K arise from the double-well potential energy surface of the hydrogen bond and quantum effects associated with the proton dynamics.     

N-甲基吡咯-2-甲醛激发态结构动力学及其溶剂效应的共振拉曼光谱和密度泛函理论研究

获取了覆盖N-甲基吡咯-2-甲醛(NMPCA)A-带和B-带电子吸收共7个激发波长的共振拉曼光谱,并结合含时密度泛函理论(TD-DFT)方法研究了的A-带和B-带电子激发和Franck-Condon区域结构动力学.TD-B3LYP/6-311++G(d,p)计算表明:A-带和B-带电子吸收的跃迁主体为π→π*.共振拉曼光谱可以指认为,11-13振动模式(A-带激发)或者7-11振动模式(B-带激发)的基频、倍频和组合频,其中C=O伸缩振动(ν7)、环的变形振动+N1-C6伸缩振动(ν17)、环的变形振动(ν21)和C6-N1-C2/C2-C3-C4不对称伸缩振动(ν14)占据了绝大部分.这表明NMPCA的Sπ激发态结构动力学主要沿C=O伸缩振动、环的变形振动和环上N1-C6伸缩振动等反应坐标展开.在同一溶剂的共振拉曼光谱中随激发波长由长变短,ν7与ν14的强度比呈现出由强变弱再变强的现象,这种变化规律被认为与Franck-Condon区域Sn/Sπ态混合或势能面交叉有关.溶剂对Sn/Sπ态混合或势能面交叉具有调控作用.     

Vibrational dynamics of acetate in D2O studied by infrared pump-probe spectroscopy

Solute-solvent interactions between acetate and D(2)O were investigated by vibrational spectroscopic methods. The vibrational dynamics of the COO asymmetric stretching mode in D(2)O was observed by time-resolved infrared (IR) pump-probe spectroscopy. The pump-probe signal contained both decay and oscillatory components. The time dependence of the decay component could be explained by a double exponential function with time constants of 200 fs and 2.6 ps, which are the same for both the COO asymmetric and symmetric stretching modes. The Fourier spectrum of the oscillatory component contained a band around 80 cm(-1), which suggests that the COO asymmetric stretching mode couples to a low-frequency vibrational mode with a wavenumber of 80 cm(-1). Based on quantum chemistry calculations, we propose that a bridged complex comprising an acetate ion and one D(2)O molecule, in which the two oxygen atoms in the acetate anion form hydrogen bonds with the two deuterium atoms in D(2)O, is the most stable structure. The 80 cm(-1) low-frequency mode was assigned to the asymmetric stretching vibration of the hydrogen bond in the bridged complex.     

Exploring the Vibrational Side of Spin‐Phonon Coupling in Single‐Molecule Magnets via 161Dy Nuclear Resonance Vibrational Spectroscopy

Synchrotron‐based nuclear resonance vibrational spectroscopy (NRVS) using the Mössbauer isotope ¹⁶¹Dy has been employed for the first time to study the vibrational properties of a single‐molecule magnet (SMM) incorporating Dy^III, namely [Dy(Cy₃PO)₂(H₂O)₅]Br₃?2 (Cy₃PO)?2 H₂O ?2 EtOH. The experimental partial phonon density of states (pDOS), which includes all vibrational modes involving a displacement of the Dy^III ion, was reproduced by means of simulations using density functional theory (DFT), enabling the assignment of all intramolecular vibrational modes. This study proves that ¹⁶¹Dy NRVS is a powerful experimental tool with significant potential to help to clarify the role of phonons in SMMs.     

Conformational dependence of intramolecular vibrational redistribution in methanol

Previous state-selected spectra of methanol in the 5nu(1) OH stretch overtone region [O. V. Boyarkin, T. R. Rizzo, and D. S. Perry, J. Chem. Phys. 110, 11346 (1999)] revealed a structure indicating an intramolecular vibrational redistribution on three time scales. Whereas in that work, methanol in the 5nu(1) bright state was prepared close to the staggered conformation, methanol in the "partially eclipsed" conformation is prepared here by double resonance excitation through a torsionally excited intermediate state. The excited molecules are detected by infrared laser assisted photofragment spectroscopy. In partially eclipsed methanol, the strong coupling of the nu(1) OH stretch to the nu(2) CH stretch becomes weaker, but the coupling responsible for the widths of the narrowest features becomes stronger.     

O(~1D)+Si(CH_3)_3Cl反应生成振动激发的OH(υ≤5)

实验光谱学和理论计算都发现,“重原子”能隔离分子中的某些振动能景,如SiH_4中Si—H振动泛频的“局域模”.Roger 等在研究F 原子与M(CH_2CH=CH_2)_4(M=Sn,Ge)的反应中,发现了Sn,Ge 对过剩能量转移到其它部分有强烈的阻碍作用(在中间态的寿命时间内).最近,在研究O(~1D)+M(CH_3)_4生成OH(v)反应中,观测到类似的现象.M=C 时,Lutz 用激光诱导荧光方法检测OH 的振动分布,振动是冷的,v=1与v=0的布居比为0.05,     

ESR and resonance Raman spectroscopic studies of peroxide intermediates derived from iron diazaoxacyclononane

A peroxide-Fe3+ intermediate generation during the Fenton reaction of iron chelate involving a ligating N,N'-di-2-picolyl-4, 7-diaza-1-oxacyclononane (DPC), H2O2/[Fe2+ DPC]2+, is reported. The identity of this peroxide complex is confirmed by resonance Raman (RR) and electron spin resonance (ESR) spectroscopies. The RR spectrum of [Fe2+ DPC]2+ treated with H2O2 shows a frequency at 854 cm(-1) ascribable to v(O-O) vibrational modes of the peroxide-Fe3+ complex with a side-on geometry. On the other hand, the ESR spectrum of H2O2/[Fe2+ DPC]2+ acquired at 77 K exhibits the resonance transition at g = 2.196 and 2.017 due to the peroxide-Fe3+ complex with an axial symmetry. It has been concluded that the H2O2/[Fe2+ DPC]2+ reaction proceeds by rapid bonding of H2O2 to an open coordination site on the central Fe2+ cation.     

Structural integration of tellurium oxide into mixed-network-former glasses: connectivity distribution in the system NaPO(3)-TeO(2).

Sodium phosphate tellurite glasses in the system (NaPO(3))(x)(TeO(2))(1-) (x) were prepared and structurally characterized by thermal analysis, vibrational spectroscopy, X-ray photoelectron spectroscopy (XPS) and a variety of complementary solid-state nuclear magnetic resonance (NMR) techniques. Unlike the situation in other mixed-network-former glasses, the interaction between the two network formers tellurium oxide and phosphorus oxide produces no new structural units, and no sharing of the network modifier Na(2)O takes place. The glass structure can be regarded as a network of interlinked metaphosphate-type P(2) tetrahedral and TeO(4/2) antiprismatic units. The combined interpretation of the O 1s XPS data and the (31)P solid-state NMR spectra presents clear quantitative evidence for a nonstatistical connectivity distribution. Rather, the formation of homoatomic P--O--P and Te--O--Te linkages is favored over mixed P--O--Te connectivities. As a consequence of this chemical segregation effect, the spatial sodium distribution is not random, as also indicated by a detailed analysis of (31)P/(23)Na rotational echo double-resonance (REDOR) experiments.     

Solvent and solvent isotope effects on the vibrational cooling dynamics of a DNA base derivative

Vibrational cooling by 9-methyladenine was studied in a series of solvents by femtosecond transient absorption spectroscopy. Signals at UV and near-UV probe wavelengths were assigned to hot ground state population created by ultrafast internal conversion following electronic excitation by a 267 nm pump pulse. A characteristic time for vibrational cooling was determined from bleach recovery signals at 250 nm. This time increases progressively in H2O (2.4 ps), D2O (4.2 ps), methanol (4.5 ps), and acetonitrile (13.1 ps), revealing a pronounced solvent effect on the dissipation of excess vibrational energy. The trend also indicates that the rate of cooling is enhanced in solvents with a dense network of hydrogen bonds. The faster rate of cooling seen in H2O vs D2O is noteworthy in view of the similar hydrogen bonding and macroscopic thermal properties of both liquids. We propose that the solvent isotope effect arises from differences in the rates of solute-solvent vibrational energy transfer. Given the similarities of the vibrational friction spectra of H2O and D2O at low frequencies, the solvent isotope effect may indicate that a considerable portion of the excess energy decays by exciting relatively high frequency (>/=700 cm-1) solvent modes.     

O(1D)+Si(CH3)3Cl反应生成振动激发的OH(ν≤3)

The vibrationally excited OH(v) from the reaction of O(~1D)+Si(CH_3)_3Cl was observed by UV laser photolysis/FTIR emission spectroscopy. The vibrational number was only up to 3 with a ratio of 1:0.8:0.1 for v=1:2:3. Comparing this result with the similar reaction of O(~1D)+Si(CH_3)_4 which OH(v) vibrational number was high up to 4 with a ratio of 1:1:1:0.3 for v=1:2:3:4 under the same experimental conditions, it was found that the substitution of Cl for CH_3 affected the extent of heavy Si atom blocking the energy migration in a molecule. This results identifies the prediction that the characteristic of electrons in central atom plays an important role in intramolecular energy transfer.     

Direct identification and decongestion of Fermi resonances by control of pulse time ordering in two-dimensional IR spectroscopy

We show that it is possible to both directly measure and directly calculate Fermi resonance couplings in benzene. The measurement method used was a particular form of two-dimensional infrared spectroscopy (2D-IR) known as doubly vibrationally enhanced four wave mixing. By using different pulse orderings, vibrational cross peaks could be measured either purely at the frequencies of the base vibrational states or split by the coupling energy. This capability is a feature currently unique to this particular form of 2D-IR and can be helpful in the decongestion of complex spectra. Five cross peaks of the ring breathing mode nu13 with a range of combination bands were observed spanning a region of 1500-4550 cm(-1). The coupling energy was measured for two dominant states of the nu13+nu16 Fermi resonance tetrad. Dephasing rates were measured in the time domain for nu13 and the two (nu13+nu16) Fermi resonance states. The electronic and mechanical vibrational anharmonic coefficients were calculated to second and third orders, respectively, giving information on relative intensities of the cross peaks and enabling the Fermi resonance states of the combination band nu13+nu16 at 3050-3100 cm(-1) to be calculated. The excellent agreement between calculated and measured spectral intensities and line shapes suggests that assignment of spectral features from ab initio calculations is both viable and practicable for this form of spectroscopy.     

Energy transfer in single hydrogen-bonded water molecules.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/HDO and acetone dissolved in carbon tetrachloride by probing the response of the O-H stretching vibrations with linear mid-infrared spectroscopy and femtosecond mid-infrared pump-probe spectroscopy. We find that the hydrogen bonds in these complexes break and reform with a characteristic time scale of approximately 1 ps. These hydrogen-bond dynamics are observed to play an important role in the equilibration of vibrational energy over the two O-H groups of the H2O molecule. For both H2O and HDO, the O-H stretching vibrational excitation relaxes with a time constant of 6.3+/-0.3 ps, and the molecular reorientation has a time constant of 6+/-1 ps.