Independent component analysis applied to diffusion‐ordered spectroscopy: separating nuclear magnetic resonance spectra of analytes in mixtures

Nuclear magnetic resonance spectrum of a mixture contains the overall peaks of all the analytes. It is impossible to perform structural assignment on the mixture without the knowledge of individual spectra of the components. Spectral separation is thus an important means of teasing out pure components of a mixture before spectral assignment. We propose a strategy called diffusion‐ordered independent component analysis (DIFFICA) to achieve this task. This strategy applies independent component analysis algorithms to diffusion‐ordered spectroscopy (DOSY) to extract spectra of pure components in a mixture. DIFFICA was tested in a simulation and experimentally in two three‐component systems with and without water suppression, in 1D and 2D DOSY data. Pure spectra were achieved in both cases. The selection of diffusion parameters to guarantee pure spectra is guided by the distance correlation between separated spectra. Copyright © 2012 John Wiley & Sons, Ltd.     

Determination of partition coefficient of spin probe between different lipid membrane phases

Model lipid membranes made from binary mixtures of dimyristoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DMPC/DPPC) and dimyristoylphosphatidylcholine/cholesterol (DMPC/Chol) exhibit coexistence of diverse lipid phases at appropriate temperature and composition. Since lipids in different phases show different structural and motional properties, it is expected that the corresponding spin probe electron paramagnetic resonance (EPR) spectra will be superposition of several spectral components. From comparison of proportions of spectral components of the EPR spectrum with the fractions of the corresponding lipid phases obtained from known phase diagrams the partition coefficient of spin probe methyl ester of 5-doxyl palmitate between different lipid phases was determined. The results indicate that the used spin probe partitions approximately equally between different phases.     

Ultrafast two-dimensional infrared vibrational echo chemical exchange experiments and theory

Ultrafast two-dimensional (2D) infrared vibrational echo experiments and theory are used to examine chemical exchange between solute-solvent complexes and the free solute for the solute phenol and three solvent complex partners, p-xylene, benzene, and bromobenzene, in mixed solvents of the partner and CCl4. The experiments measure the time evolution of the 2D spectra of the hydroxyl (OD) stretching mode of the phenol. The time-dependent 2D spectra are analyzed using time-dependent diagrammatic perturbation theory with a model that includes the chemical exchange (formation and dissociation of the complexes), spectral diffusion of both the complex and the free phenol, orientational relaxation of the complexes and free phenol, and the vibrational lifetimes. The detailed calculations are able to reproduce the experimental results and demonstrate that a method employed previously that used a kinetic model for the volumes of the peaks is adequate to extract the exchange kinetics. The current analysis also yields the spectral diffusion (time evolution of the dynamic line widths) and shows that the spectral diffusion is significantly different for phenol complexes and free phenol.     

Polarization dependent resonant x-ray emission spectroscopy of D2O and H2O water: assignment of the local molecular orbital symmetry

The polarization dependence of the split two peaks in the lone-pair region in the x-ray emission spectra has been determined at several different excitation energies for both D(2)O and H(2)O water. In contrast to predictions based on a narrow range of local water structures where the two peaks would be of different molecular orbital symmetry and arise from, respectively, intact and dissociated molecules, we show that the two peaks in the lone-pair region are both of lone-pair 1b(1) orbital symmetry. The results support the interpretation that the two peaks appear due to fluctuations between two distinct different main structural environments.     

Two-dimensional cross-spectral correlation analysis and its application to time-resolved Fourier transform emission spectra of transient radicals

A spectral analysis method, based on the generalized two-dimensional (2D) vibrational spectra correlation analysis, is developed for deciphering the correlation among the spectral peaks of two different spectra. This 2D cross-spectral correlation (2DCSC) analysis is aimed at revealing the vibrational features associated with a common species in two spectra, each obtained from a system containing multiple species with at least one common species. The cross-spectral correlation is based on the premise that the spectral features of the same species should have the same time and frequency responses toward similar perturbations. The effectiveness of the cross-spectral correlation analysis is first illustrated with model systems, with spectral peaks decaying linearly or exponentially with time, before being applied to analyzing time-resolved emission spectra obtained, by a Fourier transform IR spectrometer, for samples consisting of the vibrationally excited transient cyanooxomethyl radical (OCCN). 2DCSC among the three different sets of time-resolved spectra collected following the photodissociation of three different precursor molecules of OCCN, respectively, allows the identification of the CN and CO stretching modes of this radical.     

Two-dimensional correlation spectroscopic studies on coordination between carbonyl group of butanone and metalions

Two dimensional asynchronous spectra were used to characterize coordination between carbonyl group of butanone and metal ions by using an approach proposed in our recent paper.Spectral variation of n-π~*transition band of carbonyl group is used to probe the coordination even if metal ions does not possess any characteristic peak in spectra.Experimental results indicate that Ca~(2+) and Al~(3+) show considerable ability to coordinate with the carbonyl group of butanone and bring about spectral variation of the n-π~*transition band,which is manifested by cross peaks in 2D asynchronous spectra.     

Chemometric approach in quantification of structural identity/similarity of proteins in biopharmaceuticals

We present a chemometrics study in which we show the identity or degree of similarity of 3D protein structures of various G-CSF (Granulocyte Colony-Stimulating Factor) isolates. The G-CSF isolates share the same amino acid sequence, but the preparation was carried out by somehow diverse technologies. The comparison of 3D structures was made on the basis of 2D NMR NOESY (Nuclear Overhauser Enhancement Spectroscopy) spectra of proteins. In searching for the most appropriate criteria to determine the identity or degree of similarity of selected spectral regions of different isolates, two methods for quantitative evaluation of identity/similarity were used. The first method compares all peaks in the two investigated protein spectral regions; the extent of peaks that overlap is determined. The second method includes spectral invariants originating from graph theory. The criteria of identity/similarity were calculated from graphs, derived from a collection of up to 200 peaks of investigated 2D NMR spectral region. The peaks were linked into a graph according to the sequential nearest neighborhoods. According to the first method all peaks were relevant, considering that spectral noise was previously removed; the largest similarity was found between the protein of a commercially available G-CSF drug and one of the three new isolates produced in the laboratory. The second method indicated that the pairwise similarity of the three new isolates is larger than the similarity of any of the new isolates with the commercially available drug. This is an expected result taking into account that the new isolates are produced by the same technology, while the commercial product has additives for long-term storage that could not be completely compensated. The proposed measure of similarity may help the developers of biosimilar products to optimize the controllable parameters of the production technology and eventually to argue the identity of the new isolate in comparison with the originator commercial product.     

二维相关分析中参考谱的选择对分离重叠峰的影响

二维相关光谱是一项将光谱强度看作两个独立的光谱变量的函数的技术, 它是由动态光谱经过数学转化后得到的. 在扰动过程中, 动态光谱等于实际测得的光谱减去参考谱, 参考谱的选择是任意的, 甚至可以为0, 但是在实际应用时, 人们逐渐发现参考谱的选择会对二维相关光谱产生一定的影响. 本篇文章采用模拟的方法, 建立光谱模型, 光谱强度按e指数形式单调变化, 比较以平均谱为参考谱和不设参考谱得到的二维相关光谱图, 分析它们的区别, 在不同参考谱条件下, 利用二维相关光谱分离重叠峰, 得到的结果也不相同, 将两种条件综合利用可以得到更多更正确的信息.     

Determination of relative rate of spectral events by novel modification of two-dimensional correlation spectroscopy

Sign of two-dimensional (2D) correlation peaks provides information on sequence of spectral events. This information is related to molecular mechanism of changes in a given system. Recently, few papers addressing the problems with interpretation of the sign of 2D correlation peaks have been published. To overcome these problems, a modification of the generalized 2D correlation method has been proposed. This method compares variations in the dynamic spectrum with a linear change at a reference point. The rates of spectral responses at individual wavenumbers are proportional to magnitudes of the peaks in the slice of asynchronous spectrum at the reference point. This way, analysis of complex 2D contour plots is replaced by a simple examination of one-dimensional (1D) slice spectrum. In spite of reduced ability of the resolution enhancement, in special cases the proposed method provides information not accessible from the classical 2D correlation analysis. At first, the principles of this method are shown with the synthetic data. Next, the influence of spectral separation, band width and position changes on the slice spectrum is evaluated. Finally, the proposed approach is applied to the experimental spectra of two hydrogen-bonded systems.     

Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association

Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic potential present at the surface of biological model membranes, the electrostatic charge distribution across the membrane interface, and changes that occur upon peptide association. The spectral resolution in (31)P and (14)N MAS NMR spectra is sufficient to probe directly the negatively charged phosphate and positively charged choline segment of the electrostatic P(-)-O-CH(2)-CH(2)-N(+)(CH(3))(3) headgroup dipole of zwitterionic DMPC (dimyristoylphosphatidylcholine) in mixed-lipid systems. The isotropic shifts report on the size of the potential existing at the phosphate and ammonium group within the lipid headgroup while the chemical shielding anisotropy ((31)P) and anisotropic quadrupolar interaction ((14)N) characterize changes in headgroup orientation in response to surface potential. The (31)P/(14)N isotropic chemical shifts for DMPC show opposing systematic changes in response to changing membrane potential, reflecting the size of the electrostatic potential at opposing ends of the P(-)-N(+) dipole. The orientational response of the DMPC lipid headgroup to electrostatic surface variations is visible in the anisotropic features of (14)N and (31)P NMR spectra. These features are analyzed in terms of a modified "molecular voltmeter" model, with changes in dynamic averaging reflecting the tilt of the C(beta)-N(+)(CH)(3) choline and PO(4)(-) segment. These properties have been exploited to characterize the changes in surface potential upon the binding of nociceptin to negatively charged membranes, a process assumed to proceed its agonistic binding to its opoid G-protein coupled receptor.     

Heterogeneity of water at the phospholipid membrane interface

Femtosecond infrared (IR) two-color pump-probe experiments were used to investigate the nonlinear response of the D2O stretching vibration in weakly hydrated dimyristoyl-phosphatidylcholine (DMPC) membrane fragments. The vibrational lifetime is comparable to or longer than that in bulk D2O and is frequency dependent, as it decreases with increasing probe frequency. Also, the lifetime increases when the water content of the sample is lowered. The measured lifetimes range between 903 and 390 fs. A long-lived spectral feature grows in following the excitation and is attributed to photoinduced D-bond breaking. The photoproduct spectrum differs from the steady state difference Fourier transform infrared (FTIR) spectrum, showing that the full thermalization of the excitation energy happens on a much longer time scale than the time interval considered (12 ps). Further evidence of the inhomogeneous character of the water residing in the polar region of the bilayer comes from the spectral anisotropy. The water molecules absorbing on the low frequency side of the absorption band show no decay at all of the anisotropy, while an ultrafast partial decay appears when the high frequency side of the spectrum is probed. The overall behavior differs remarkably from that observed with similar experiments in bulk water and in water segregated in inverse micelles. In weakly hydrated phospholipid membranes, water molecules are present mostly as isolated species, prevalently involved in strong, rigid, and persistent hydrogen bonds with the polar groups of the bilayer molecules. This specific character appears to have a direct effect on the structural stability and thermal properties of the membrane.     

Solvation and thermalization of electrons generated by above-the-gap (12.4 eV) two-photon ionization of liquid H2O and D2O

Temporal evolution of transient absorption (TA) spectra of electrons generated by above-the-gap (12.4 eV total energy) two-photon ionization of liquid H2O and D2O has been studied on femto- and picosecond time scales. The spectra were obtained at intervals of 50 nm between 0.5 and 1.7 mum. Two distinct regimes of the spectral evolution were observed: t < 1 ps and t > 1 ps. In both of these regimes, the spectral profile changes considerably with the delay time of the probe pulse. The "continuous blue shift" and the "temperature jump" models, in which the spectral profile does not change as it progressively shifts, as a whole, to the blue, are not supported by our data. Furthermore, no p-state electron, postulated by several authors to be a short-lived intermediate of the photoionization process, was observed by the end of the 300 fs, 200 nm pump pulse. For t < 1 ps, two new TA features (the 1.15 microm peak and 1.4 mum shoulder) were observed for the electron in the spectral region where O-H overtones appear in the spectra of light water. These two features were not observed for the electron in D2O. The 1.4 mum peak observed in D2O may be the isotope-shift analogue of the 1.15 microm feature in H2O. Vibronic coupling to the modes of water molecules lining the solvation cavity is a possible origin of these features. On the sub-picosecond time scale, the absorption band of solvated electron progressively shifts to the blue. At later delay times (t > 1 ps), the position of the band maximum is "locked", but the spectral profile continues to change by narrowing on the red side and broadening on the blue side; the oscillator strength is constant within 10%. The time constant of this narrowing is ca. 0.56 ps for H2O and 0.64 ps for D2O. Vibrational relaxation and time-dependent decrease in the size and sphericity of the solvation cavity are suggested as possible causes for the observed spectral transformations in both of these regimes.     

Two-dimensional infrared spectral signatures of 3(10)- and alpha-helical peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.     

Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide

The linear IR and two-dimensional (2D) IR spectra of the amide-I modes of the 12-residue beta-hairpin peptide tryptophan zipper-2 (SWTWENGKWTWK) and its two 13C isotopomers were simulated, with local mode frequencies evaluated by two solution-phase peptide amide-I frequency maps proposed recently: an electrostatic potential map and an electrostatic field map. Both maps predict a set of nondegenerate local amide-I mode transition energies for the hairpin. Spectral simulations using both maps predict the main spectral features of the linear IR and 2D IR experimental results of the (13)C-labeled and -unlabeled hairpin. The radial distribution functions obtained using trajectories from classical molecular dynamics simulations demonstrate different water distributions at different sites of the hairpin. Our results suggest that the observed difference of the (13)C-shifted band, including its peak position and frequency distributions for different isotopomers, in both linear IR and 2D IR spectra, is likely to be due to the difference in the local environment of the solvated peptide. Ab initio density functional theory calculations show a residue-independent (13)C shift of the amide-I mode, further supporting the result. The variations of these shifts are attributed to the residue level heterogeneity of the electrostatic environment of the peptide. Our results show that 2D IR of peptide with single (13)C isotopic labeling can be used to probe the electrostatic environment of the peptide local structure.     

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.     

LiMn_2O_4中锂离子扩散系数与充/放电次数的关系

通过容量间歇滴定技术(CITT)对不同电压、不同循环次数下,锂离子在尖晶石LiMn_2O_4中的固相扩散系数进行了研究.结果表明,锂离子在尖晶石LiMn_2O_4正极材料中的固相扩散系数在3.95V和4.12V左右存在两个极小峰,随着循环次数的增加,这两个峰逐渐平坦,并且整体上固相扩散系数呈增大趋势,表明锂离子在LiMn_2O_4中重复脱/嵌时具有自我增强扩散的能力.     

Dynamic structures of aqueous oxalate and the effects of counterions seen by 2D IR

Two dimensional vibrational echo spectra of oxalate in the carboxylate asymmetric stretch region in D(2)O show two transitions having anomalously slow spectral diffusion and a third transition having relaxation properties typical of the free carboxylate ion. Quantitative analysis of the frequency shifts of the carboxylate asymmetric stretch modes caused by a singly charged cation in the oxalate hydration shell supports that ion pairs can be responsible for these new transitions. Experimental evidence and DFT calculations are consistent with oxalate forming a mixture of "side-on" and "end on" contact ion pairs wherein the carboxylate groups are protected from mobile heavy water molecules.     

LiMn2O4中锂离子扩散系数与充/放电次数的关系

通过容量间歇滴定技术（CITT）对不同电压、不同循环次数下，锂离子在尖晶石LiMn₂O₄中的固相扩散系数进行了研究. 结果表明，锂离子在尖晶石LiMn₂O₄正极材料中的固相扩散系数在3.95 V和4.12 V左右存在两个极小峰，随着循环次数的增加，这两个峰逐渐平坦，并且整体上固相扩散系数呈增大趋势，表明锂离子在LiMn₂O₄中重复脱/嵌时具有自我增强扩散的能力.     

Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe structural dynamics under thermal equilibrium conditions on time scales ranging from femtoseconds to approximately 100 ps and longer. One of the important uses of 2D-IR spectroscopy is to monitor the dynamical evolution of a molecular system by reporting the time dependent frequency fluctuations of an ensemble of vibrational probes. The vibrational frequency-frequency correlation function (FFCF) is the connection between the experimental observables and the microscopic molecular dynamics and is thus the central object of interest in studying dynamics with 2D-IR vibrational echo spectroscopy. A new observable is presented that greatly simplifies the extraction of the FFCF from experimental data. The observable is the inverse of the center line slope (CLS) of the 2D spectrum. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first electric field-matter interaction. The CLS varies from a maximum of 1 to 0 as spectral diffusion proceeds. It is shown analytically to second order in time that the CLS is the T(w) (time between pulses 2 and 3) dependent part of the FFCF. The procedure to extract the FFCF from the CLS is described, and it is shown that the T(w) independent homogeneous contribution to the FFCF can also be recovered to yield the full FFCF. The method is demonstrated by extracting FFCFs from families of calculated 2D-IR spectra and the linear absorption spectra produced from known FFCFs. Sources and magnitudes of errors in the procedure are quantified, and it is shown that in most circumstances, they are negligible. It is also demonstrated that the CLS is essentially unaffected by Fourier filtering methods (apodization), which can significantly increase the efficiency of data acquisition and spectral resolution, when the apodization is applied along the axis used for obtaining the CLS and is symmetrical about tau=0. The CLS is also unchanged by finite pulse durations that broaden 2D spectra.     

Ultrafast Structural Dynamics of Biomolecules Examined by Multiple‐Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L ‐α‐glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal‐mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two‐dimensional infrared (2D IR) spectra, which are simulated using time‐domain third‐order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.