Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

Simply enhancing throughput of free‐flow electrophoresis via organic‐aqueous environment for purification of weak polarity solute of phenazine‐1‐carboxylic acid in fermentation of Pseudomonas sp. M18

Herein, a simple novel free‐flow electrophoresis (FFE) method was developed via introduction of organic solvent into the electrolyte system, increasing the solute solubility and throughput of the sample. As a proof of concept, phenazine‐1‐carboxylic acid (PCA) from Pseudomonas sp. M18 was selected as a model solute for the demonstration on feasibility of novel FFE method on account of its faint solubility in aqueous circumstance. In the developed method, the organic solvent was added into not only the sample buffer to improve the solubility of the solute, but also the background buffer to construct a uniform aqueous‐organic circumstance. These factors of organic solvent percentage and types as well as pH value of background buffer were investigated for the purification of PCA in the FFE device via CE. The experiments revealed that the percentage and the types of organic solvent exerted major influence on the purification of PCA. Under the optimized conditions (30 mM phosphate buffer in 60:40 (v/v) water‐methanol at an apparent pH 7.0, 3.26 mL/min background flux, 10‐min residence time of injected sample, and 400 V), PCA could be continuously purified from its impurities. The flux of sample injection was 10.05 μL/min, and the recovery was up to 93.7%. An 11.9‐fold improvement of throughput was found with a carrier buffer containing 40% (v/v) methanol, compared with the pure aqueous phase. The developed procedure is of evident significance for the purification of weak polarity solute via FFE.     

背景吸收强度可调控与扣除干扰组分影响的红外光谱测量方法

多组分混合物的红外光谱由于特征谱带的重叠或部分重叠而给谱峰的归属辨认带来极大的困难。本研究通过扫描两个背景样品(纯KBr压片(1)和KBr+C18TCNQ压片(2))实时合成一系列背景单光束谱。每个背景单光束谱既含有背景样品1的贡献也含有背景样品2的贡献。干扰组分C18TCNQ在系列背景谱中的吸收强度随扫描次数变化而改变。当待测混合物和背景样品中干扰组分的吸收强度相等时,就可以完全扣除干扰组分的影响。本测量方法用于硬脂酸与C18TCNQ混合物中扣除硬脂酸(或者C18TCNQ)的干扰,得到令人满意的结果。合成背景样品中干扰组分的含量在测量时成为与扫描次数有关的变量,为扣除干扰组分的影响提供了直接便利的红外光谱测量方法。     

Advantages of time-resolved difference X-ray solution scattering curves in analyzing solute molecular structure

Time-resolved X-ray solution scattering provides a powerful method for investigating reaction dynamics in the solution phase. Since X-rays scatter from all atoms in the solution sample, the scattering intensity is contributed from not only the solute but also the solvent and the solute–solvent cross terms. For a typical concentration the solvent molecules outnumber the solute molecules and thus the relative sensitivity of the scattering intensity to the solute structure is extremely low. To increase the structural sensitivity to the solute and to extract only the signal from structural changes, time-resolved difference scattering signal is obtained by subtracting the original raw scattering curve at a negative reference time delay from that at a positive time delay. Here we show and emphasize that time-resolved difference X-ray scattering curves generally exhibit higher structural sensitivity to the solute molecular structure and lower influence from experimental background and imperfection of theory than original raw scattering curves. These characteristics justify the validity of fitting models to difference curves to obtain transient structural information even when the magnitude of the time-resolved difference curves is smaller than the discrepancy between the theory and experiment for the original scattering curve. We considered small molecules and proteins in solution probed by time-resolved X-ray solution scattering.     

Modeling absorption spectra of molecules in solution

The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute–solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute–solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. We also present our recent results combining the vertical excitation energies computed from an ensemble of solute–solvent configurations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution.     

Resolving the emission times of solute and solvent four-wave mixing signals by spectral interferometry

Electric field-resolved transient grating measurements are used to distinguish the four-wave mixing signal emission from a resonant solute and a non-resonant solvent. The two components of the solution (i.e., solute and solvent) emit signal fields at different times with respect to the arrival of the probe pulse to the sample. This gives rise to a recurrence in the temporal profile of the total signal field. We show that the origin of this interference is the difference in relaxation time scales of the holographic gratings associated with the solute and solvent. The grating of the resonant solute relaxes on the time scale of a few picoseconds due to depopulation of its excited electronic state, whereas the electronic polarizability response of the solvent relaxes on the femtosecond time scale. This separability of responses is a general phenomenon that is particularly useful for studying weakly absorbing solute dynamics in polarizable solvents.     

Effects of pressure and solvents on the infrared absorption intensities of C-I stretching modes of methyl and ethyl iodides in solutions

We have investigated effects of pressure and solvents on infrared intensities of methyl and ethyl iodides in solutions using a hydrostatic high-pressure cell with synthetic diamond windows. We focused on the absolute intensity of the C-I stretching mode, which was measured in carbon disulfide solvent up to 300MPa and at 293K, and in n-hexane solvent at 298K. For comparison, we investigated the effect of solvents on the absorption intensity. Effects of pressure and solvents on the infrared intensity were analyzed using two electrostatic models, which assume the shape of solute cavity as sphere or spheroid. The latter model is approximately in agreement with both effects on the intensity, particularly, for the pressure effect. This paper demonstrated that the electrostatic model taking the shape of the cavity into account is useful to explain the medium effect on the infrared intensity and also suggests that more improved models could provide information of the solvation structure from the medium effect on the infrared intensity.     

丙酮分子n→π*跃迁光谱的平均溶剂静电势/分子动力学方法研究

采用量子力学/分子动力学方法研究了具体溶剂分子结构对溶质光谱行为的静电影响. 通过拟合溶质所处外电场和引入溶剂分子极化率, 考虑了溶质溶剂分子之间的相互极化效应, 得到合理的溶质和溶剂分子的电荷分布. 经过严格推导发现, 在传统的显溶剂模型中, 平衡和非平衡溶剂化能表达式均未考虑溶剂分子永久偶极弹簧能的贡献. 因此, 在正确计算永久偶极弹簧能的基础上, 重新建立了溶剂化能的表达式和新的吸收/发射光谱移动公式. 采用修改后的ASEP/MD程序, 计算得到了与实验值比较吻合的丙酮在水溶液中n→π*跃迁的光谱移动值, 验证了新公式的合理性.     

Time-dependent density functional theory/discrete reaction field spectra of open shell systems: The visual spectrum of [FeIII(PyPepS)2]- in aqueous solution

We report the calculated visible spectrum of [FeIII(PyPepS)2]- in aqueous solution. From all-classical molecular dynamics simulations on the solute and 200 water molecules with a polarizable force field, 25 solute/solvent configurations were chosen at random from a 50 ps production run and subjected the systems to calculations using time-dependent density functional theory (TD-DFT) for the solute, combined with a solvation model in which the water molecules carry charges and polarizabilities. In each calculation the first 60 excited states were collected in order to span the experimental spectrum. Since the solute has a doublet ground state several excitations to states are of type "three electrons in three orbitals," each of which gives rise to a manifold of a quartet and two doublet states which cannot properly be represented by single Slater determinants. We applied a tentative scheme to analyze this type of spin contamination in terms of Delta and Delta transitions between the same orbital pairs. Assuming the associated states as pure single determinants obtained from restricted calculations, we construct conformation state functions (CFSs), i.e., eigenfunctions of the Hamiltonian Sz and S2, for the two doublets and the quartet for each Delta,Delta pair, the necessary parameters coming from regular and spin-flip calculations. It appears that the lower final states remain where they were originally calculated, while the higher states move up by some tenths of an eV. In this case filtering out these higher states gives a spectrum that compares very well with experiment, but nevertheless we suggest investigating a possible (re)formulation of TD-DFT in terms of CFSs rather than determinants.     

Vibrational analysis of 2-[4-(<Emphasis Type="Italic"> N</Emphasis> -dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole

The infrared absorption spectra of 2-[4-( N -dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole (also denoted AF51) in solution and in the solid state as well as the solid-state Raman spectrum of the powdered compound are compared with the infrared linear dichroic (LD) spectra recorded at two orthogonal polarizations. The IR-LD spectra were measured in an anisotropic solvent-the nematic liquid crystal ZLI-1695 (Merck). The solvent spectrum taken under precisely the same experimental conditions and polarized radiation azimuths was subtracted from the polarized sample spectra in order to achieve pure oriented spectra of the compound studied. These spectra were further processed using a stepwise reduction procedure that allows for assignment of vibrational modes having mutually orthogonal dipole moments.     

Sample Solvent as Analyte in High Performance Liquid Chromatography

Abstract

Solvents vary in their behavior in high performance liquid chromatography (HPLC). Water and methanol, among others, are widely used in the mobile phase as well as solvents for the solute. Few reports indicate that the solvent used for the solute can behave as an analyte. Normally, it is generally accepted that the solute solvent, a non-constituent of the mobile phase will be the first eluent. However, a solvent which is a component of the sample can show up as an unexpected peak with its own identity. This solvent may show a similar retention time as some of the unknown components of the sample. This indicates that in some cases the quantitative results may be the sum of the absorptivity of the solute and solvent used for the sample. It is assumed that some solvents show no absorption in the ultraviolet region at which the analysis is being conducted. Depending on the mobile phase composition some solvents can be detected at the wavelengts or wavelengths used for analysis. Water, ethylacetate, and methanol showed absorption at 210 nm when present in the sample being analyzed with a mobile phase of acetonitrile-methanol using a C₁₈ column. These solvents overlapped or showed retention times the same as estriol and testosterone.     

Edge excitation red shift and energy migration in quinine bisulphate dication

Photoinduced excited state dynamical processes in quinine sulphate dication (QSD) have been studied over a wide range of solute concentrations using steady state and nanosecond time-resolved fluorescence spectroscopic techniques. The edge excitation red shift (EERS) of emission maximum, emission wavelength dependence of fluorescence lifetimes and the time dependence of emission maximum are known to occur due to the solvent relaxation process. With increase in solute concentration, the emission spectrum shifts towards the lower frequencies accompanied with decrease in fluorescence intensity, however, absorption spectrum remains unchanged. A decrease in EERS, fluorescence lifetimes, time dependent fluorescence Stokes shift (TDFSS), fluorescence polarization and the solvent relaxation time (τ_r) is observed with the increase in solute concentration. The process of energy migration among the QSD ions along with solvent relaxation has been found responsible for the above experimental findings.     

Measuring the change in the intermolecular Raman spectrum during dipolar solvation

We demonstrate a method to directly measure the change in the spectrum of intermolecular solvent fluctuations as a function of time after electronic excitation of a solute, and this method is applied to the dye Coumarin 102 (C102) in acetonitrile. The complete intermolecular response is captured following resonant excitation with time domain third-order Raman spectroscopy. In a previous report, we introduced this method and used it to probe one point in the intermolecular response as a function of time after solute excitation (Underwood, D. F., Blank, D. A. J. Phys. Chem. A 2003, 107 (7), 956). Here we extend this approach to recover the change in the entire intermolecular response as a function of time. To our knowledge the results provide the first direct measurement of the difference in the equilibrated intermolecular response after excitation of a solute and its evolution during a dipolar solvation event. Excitation of C102 results in a significant increase in the solvent-solute interaction due to a large increase in the dipole moment. The observed change in the intermolecular response is consistent with a rapid change in local solvent density, with intermolecular kinetic energy transfer changing the response on longer time scales. Evolution of the response exhibits a strong frequency dependence and suggests changes over longer distances at longer delay times. The measured change in the spectrum of solvent fluctuations represents a direct experimental confirmation of the breakdown of linear response and confirms predictions from molecular dynamics simulations.     

Hydrogen bond lifetimes and energetics for solute/solvent complexes studied with 2D-IR vibrational echo spectroscopy

Weak pi hydrogen-bonded solute/solvent complexes are studied with ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature-dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute/solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen-bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory.     

Tailoring noise frequency spectrum to improve NIR determinations

Near infrared spectroscopy (NIR) contains excessive background noise and weak analytical signals caused by near infrared overtones and combinations. That makes it difficult to achieve quantitative determinations of low concentration samples by NIR. A simple chemometric approach has been established to modify the noise frequency spectrum to improve NIR determinations. The proposed method is to multiply one Savitzky-Golay filtered NIR spectrum with another reference spectrum added with thermal noises before the other Savitzky-Golay filter. Since Savitzky-Golay filter is a kind of low-pass filter and cannot eliminate low frequency components of NIR spectrum, using one step or two consecutive Savitzky-Golay filter procedures cannot improve the determination of NIR greatly. Meanwhile, significant improvement is achieved via the Savitzky-Golay filtered NIR spectrum processed with the multiplication alteration before the other Savitzky-Golay filter. The frequency range of the modified noise spectrum shifts toward higher frequency regime via multiplication operation. So the second Savitzky-Golay filter is able to provide better filtering efficiency to obtain satisfied result. The improvement of NIR determination with tailoring noise frequency spectrum technique was demonstrated by both simulated dataset and two measured NIR spectral datasets. It is expected that noise frequency spectrum technique will be adopted mostly in applications where quantitative determination of low concentration sample is crucial.     

Spin amplification in solution magnetic resonance using radiation damping

The sensitive detection of dilute solute spins is critical to biomolecular NMR. In this work, a spin amplifier for detecting dilute solute magnetization is developed using the radiation damping interaction in solution magnetic resonance. The evolution of the solvent magnetization, initially placed along the unstable -z direction, is triggered by the radiation damping field generated by the dilute solute magnetization. As long as the radiation damping field generated by the solute is larger than the corresponding thermal noise field generated by the sample coil, the solute magnetization can effectively trigger the evolution of the water magnetization under radiation damping. The coupling between the solute and solvent magnetizations via the radiation damping field can be further improved through a novel bipolar gradient scheme, which allows solute spins with chemical shift differences much greater than the effective radiation damping field strength to affect the solvent magnetizations more efficiently. Experiments performed on an aqueous acetone solution indicate that solute concentrations on the order of 10(-5) that of the solvent concentration can be readily detected using this spin amplifier.     

Peculiar properties of water as solute

Water has been investigated for a long time as the most important solvent; the peculiar behavior of water as solute has been studied in binary mixtures with organic solvents, mainly exploring the whole phase diagram. In this Article, we studied the behavior of water in binary mixtures with propylene carbonate in the phase diagram region where water acts as a solute as a function of the water molar fraction X(water). Surface tension measurements, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) have been used to investigate the state of water molecules and hydrogen bonds when water is to be considered a solute instead of a solvent, and peculiar and interesting properties were discovered. The interaction of water molecules among themselves and between water and propylene carbonate has been shown to be dependent on the water concentration in the mixtures. All of the measured properties showed a break at X(water) approximately 0.15-0.20 similar to the break due to the critical micellar concentration in surfactant solutions. In particular, from the FTIR spectra, it was possible to deduce that at this concentration water has a transition from pure solute ("multimers" solvated by PC) to cosolvent ("intermediate" and "network" water).     

Photolysis-assisted, long-path FT-IR detection of air pollutants in the presence of water and carbon dioxide

Seven important air pollutants have been investigated by photolysis-assisted FT-IR spectroscopy. This technique renders invisible the spectra of water and carbon dioxide, which are two of the main concerns in long-path infrared spectroscopy. A cell, equipped with a UV lamp, was used to oxidise the analyte in the air sample and the spectrum recorded was used as a new background for the original sample spectrum. The optimum UV irradiation time and correctness of the concentrations were determined for this technique and compared with those from traditional methods. The signal-to-noise (S/N) ratios of the so-called “shadow spectra” were better than, or at least comparable to, the S/N ratios in the absorbance spectra obtained by using as background an air or an evacuated cell reference and subtraction of the spectra of water and carbon dioxide from a spectral library. The detection limits for the volatile organic compounds investigated have been improved by using this new method in which an appropriate background spectrum can be obtained quickly. The limitations of the method are that it cannot be applied to non-UV reactive compounds, such as methane, and the detection limits can be appreciably degraded when bands due to ozone in the shadow spectra overlap with those of the compounds under investigation.     

计算平均力势的理论方法

A universal theoretical framework is proposed for calculating potential of mean force (PMF) between two solute particles immersed in a solvent bath, the present method overcomes all of drawbacks of previous methods. The only input required to implement the recipe is solvent density distribution profile around a single solute particle. The universal framework is applied to calculate the PMF between two large spherical particles immersed in small hard sphere solvent bath. Comparison between the present predictions and existing simulation data shows reliability of the present recipe. Effects of solvent-solute interaction detail, solvent bulk density, and solute size on the excess PMF are investigated. The resultant conclusion is that depletion of solvent component by the solute particle induces attractive excess PMF, while gathering of solvent component by the solute particle induces repulsive excess PMF, high solvent bulk density and large solute size can strengthen the tendency of attraction or repulsion. Relevance of transition from depletion attraction to gathering repulsion with the biomolecular interaction, i.e. hydrophobic attraction and hydration repulsion, is discussed.