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.     

Simulations of X-ray absorption spectra: the effect of the solvent

We perform quantum mechanics/molecular mechanics molecular dynamics simulations on the [Pt(2)(P(2)O(5)H(2))(4)](4-) (abbreviated PtPOP) complex; in water, dimethylformamide and ethanol. These are used to calculate the ground state X-ray absorption spectrum of the complex. The structural parameters from X-ray spectra are usually extracted using a fit of the experimental data. In such simulations the solvent is neglected meaning that any effect of the local environment will be compensated for by structural changes of the solute, leading to possible discrepancies in the extracted structural parameters. Our simulations show a significant solvent effect on the spectra, which has important implications for the structural analysis of molecules in solution.     

Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations

Binding energies of ion triplets formed in ionic liquids by Li⁺ with two anions have been studied using quantum‐chemical calculations with implicit and explicit solvent supplemented by molecular dynamics (MD) simulations. Explicit solvent approach confirms variation of solute‐ionic liquid interactions at distances up to 2 nm, resulting from structure of solvation shells induced by electric field of the solute. Binding energies computed in explicit solvent and from the polarizable continuum model approach differ largely, even in sign, but relative values generally agree between these two models. Stabilities of ion triplets obtained in quantum‐chemical calculations for some systems disagree with MD results; the discrepancy is attributed to the difference between static optimized geometries used in quantum chemical modeling and dynamic structures of triplets in MD simulations. © 2015 Wiley Periodicals, Inc.     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Solvation and solvatochromism in CO2-expanded liquids. 2. Experiment-simulation comparisons of preferential solvation in three prototypical mixtures

Electronic absorption and emission spectra of 10-bis(phenylethynyl)anthracene (PEA) and coumarin 153 (C153) are measured as functions of composition along the bubble-point curve at 25 degrees C in CO2-expanded cyclohexane (c-C6H12), acetonitrile (CH3CN), and methanol (CH3OH). The nonlinear dependence of the spectral frequencies on composition suggests substantial preferential solvation of both solutes by the liquid components of these mixtures. Estimates of enrichment factors (local mole fraction of a component divided by its bulk value) based on the assumption that spectral shifts are linearly related to local composition are quite large (approximately 10) in the cases of the C153/CH3CN + CO2 and C153/CH3OH + CO2 systems at high xCO2. Computer simulations of anthracene, the chromophore of PEA, and C153 in these three CO2-expanded liquids are used to clarify the relationship between local composition and spectral shift. A semiempirical model consisting of additive electrostatic and dispersive interactions is able to capture the main features observed experimentally in all six solute/solvent combinations. The simulations show that the commonly used assumption of a linear relation between spectral shifts and local compositions grossly exaggerates the extent of preferential solvation in these mixtures. The collective nature of electrostatic solvation and the composition dependence of the solute's coordination number are shown to be responsible for the breakdown of this assumption.     

Effects of external electric field and self-aggregations on conformational transition and optical properties of azobenzene-based D-π-A type chromophore in THF solution

The influence of environments (THF solvents and electric field) and molecular self-aggregations on the structure and optical properties of 4-(4-hydroxyphenylazo)nitrobenzene has been investigated by molecular dynamics (MD) simulations and quantum chemical calculations. Long-range electrostatic effects and the hydrogen bond interactions between the solute and the THF solvent molecules lead to the augments of nonlinear optical (NLO) response by about two times from the gas phase to THF solution, accompanied by considerable red-shift of more than 40 nm in the maximum absorption wavelengths of the ground (S(0)) and low-lying excited states (S(1), S(2), and S(3)). The solvated chromophore reorients quickly (within 300 ps) under external electric field of 1.0 V/nm, even when the direction of the applied electric field is antiparallel to the dipole moment of the solute. Nonequilibrium MD simulations demonstrate that the light-induced cis-trans isomerization in THF solution and external electric field need longer relaxation time (about 1.0 ps) than that in gas phase (about 500 fs). The dipole-dipole interactions and intermolecular hydrogen bonds facilitate the self-aggregations of solute molecules in solution. The V-shaped dimer exhibits higher hyperpolarizability value by about 1.2 times of the monomer, whereas the antiparallel alignment leads to a cancellation of dipole moment and hence dramatic decrease in hyperpolarizability (one-third of the monomer). However, the Boltzmann-weighted contribution to hyperpolarizability from these two aggregations (with 82% V-shaped and 18% antiparallel) is close to that of the monomer. Orientations of D-π-A dipoles in various environments and molecular aggregations are important to modulate the optical properties of materials.     

Hydrogen bonding and solvent effects on the lowest 1(n, pi*) excitations of triazines in water

Our method for estimating solvent effects on electronic spectra in media with strong solute-solvent interactions is applied here to calculate the absorption and fluorescence solvatochromatic shifts of dilute triazines in water. First, the ab initio CASSCF method is used to estimate the gas-phase electronic excitation properties and state charge distributions; second, Monte Carlo simulations are performed to elucidate liquid structures around the ground and excited state solute; finally, the solvent shift is evaluated based on the gas-phase charge distributions and the explicit solvent structures. For the dilute triazine solutions, simulations predict one linear (different) hydrogen bond attached to each nitrogen atom. Upon the first (1)(n, pi*)electronic excitation one hydrogen bond is completely broken. For the absorption and fluorescence spectra, our calculations demonstrated that the specific solvent-solute interaction, in any electronic state, plays a critical role in the determination of solvent shifts.     

N2,O2水溶液光谱的分子动力学模拟

用分子动力学模拟方法研究了N2和O2水溶液的光谱性质．给出了能描述分子内部运动的溶质－溶剂相互作用势．对溶质和溶剂原子的速度自相关函数（VACF）作了计算．讨论了所得VACF的性质并计算了其谱密度．溶质分子振动谱出现的红移，与液态N2，O2的Raman实验结果相吻合．模拟得出的转动谱表明了溶剂分子对溶质转动运动的阻滞，模拟结果也表明VACF计算对溶液和液体光谱的研究十分有效．     

Quantum mechanics/fluctuating charge calculations for absorption spectra of aqueous green fluorescent protein chromophore

We applied the quantum mechanics/fluctuating charges (QM/FQ) method to simulate the absorption spectra of three protonated forms of p-hydroxybenzylidene imidazolone (p-HBDI) in water. Configurations of solute-solvent were generated from molecular dynamics (MD) simulation within the context of a hybrid scheme in which solute and solvents were treated at QM and molecular mechanics, respectively. Nonperiodic spherical boundary condition was used. To examine the influence on simulated spectra coming from the geometrical relaxation of solute, the MD simulations were carried out for two cases: frozen and flexible molecular geometry of solute. As a result of our calculations, the simulations using the flexible solute's structure delivered vertical excitation energies closer to experimental data than those of a frozen solute, especially for the neutral case. For spectral broadening, changing from fixed geometry of solute to a flexible one led to a significant increase for both neutral and anionic forms of p-HBDI, but no effect happened for the cationic one.     

Structure and dynamics of the solvated electron in alcohols from resonance Raman spectroscopy

Resonance Raman (RR) spectroscopy is used to probe the structure and excited-state dynamics of the solvated electron in the primary liquid alcohols methanol (MeOH), ethanol (EtOH), n-propanol (n-PrOH), and n-butanol (n-BuOH). The strong resonance enhancements (>or=10(4) relative to pure solvent) of the libration, CO stretch, COH bend, CH3 bend, CH2 bend, and OH stretch reveal significant Franck-Condon coupling of the intermolecular and intramolecular vibrational modes of the solvent to the electronic excitation of the solvated electron. All enhanced bands are fully accounted for by a model of the solvated electron that is comprised of several nearby solvent molecules that are only perturbed by the presence of the electron; no new molecular species are required to explain our data. The 340 cm(-1) downshift observed for the OH stretch frequency of e-(MeOH), relative to pure solvent, strongly suggests that the methanol molecules in the first solvent shell have the hydroxyl group directed linearly toward the excess electron density. The smaller downshifts observed for e-(EtOH), e-(n-PrOH), and e-(n-BuOH) are explained in terms of a OH group that is bent 28-40 degrees from linear. The Raman cross sections and absorption spectra are modeled, lending quantitative support for the inhomogeneous origin of the broad absorption spectra, the necessity of OH local motion in all enhanced Raman modes of the alcohols, and the dominant librational response of the solvent upon photoexcitation of the electron.     

The effects of solute-solvent electrostatic interactions on solvatochromic shifts in supercritical CO2

Solvent clustering around attractive solutes is an important feature of supercritical solvation. We examine here the effects of the local density enhancement on solvatochromic shifts in electronic absorption and emission spectra in supercritical CO2. We use molecular dynamics (MD) simulation to study the spectral line shifts for model diatomic solutes that become more polar upon electronic excitation. The electronic transition is modeled as either a change from a quadrupolar to a dipolar solute charge distribution or as an increase in the magnitude of the solute dipole. Our main focus is on the density dependence of the line shifts at 320 K, which corresponds to about 1.05 times the solvent critical temperature, Tc, but results for higher temperatures are also obtained in order to determine the behavior of the line shifts in the absence of local density enhancement. We find that the extent of local density enhancement at 1.05Tc is strongly correlated with solute-solvent electrostatic attraction and that the density dependence of the emission line shifts resembles the behavior of the effective local densities, rho(eff), obtained from the first-shell coordination numbers. The differences that are seen are shown to be due to solute-solvent orientational correlations which provide an additional source of enhancement for electrostatic solvation energies and spectral line shifts.     

Experimental probing and modeling of key sorbent-solute interactions of norephedrine enantiomers with polysaccharide-based chiral stationary phases

The key interactions of a chiral solute, norephedrine or 2-amino-1-phenyl-1-propanol (PPA), with three commercially important polysaccharide-based chiral stationary phases, amylose Tris(3,5-dimethylphenylcarbamate) (ADMPC), amylose Tris((S)-alpha-methylbenzylcarbamate) (ASMBC) and cellulose Tris(3,5-dimethylphenylcarbamate) (CDMPC) are studied in detail using different experimental techniques and molecular simulations. The HPLC retention factors of the enantiomers of PPA in n-hexane/2-propanol (90/10, v/v) at 298 K vary significantly with these sorbents. The enantioselectivities of -PPA versus +PPA are 2.4, 1.0, and 0.8 (reversal in the elution order), respectively. The observed changes in the wavenumbers and the intensities of the amide bands of these polymers in the attenuated total reflection-infrared spectroscopy (ATR-IR) spectra upon absorption of each enantiomer are different. The IR wavenumbers, and the H-bonding interaction energies of the polymer side chains with each enantiomer (polymer-solute) in four different binding configurations are estimated and ranked using the density functional theory (the DFT/B3LYP/6-311+g(d,p) level of theory). X-ray diffraction (XRD) results show that the polymer crystallinity increases significantly upon absorption of each enantiomer. The helical pitches and the inter-rod packing for these polymers are inferred from the XRD results and incorporated into the molecular dynamics (MD) simulations. The elution orders predicted for the enantiomers of PPA using MD simulations of the polymer-PPA binary systems are consistent with the chromatography results. The enantioselectivity observed in ADMPC is hypothesized to be due to having three simultaneous interactions (two H-bond and one pi-pi) of the polymer with -PPA versus two interactions (one H-bond and one pi-pi) with +PPA.     

Solvent effects on isomerization and spectral properties of photochromic-switching diarythene derivatives in polar and apolar solutions

The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.     

Molecular dynamics simulation studies of absorption in piperazine activated MDEA solution

Development of more efficient solvent solutions for removal of CO(2) from natural gas and flue gases is a major task, which contributes to improved design of process plants and leads to decreased costs for its removal. Understanding the mechanisms of CO(2) absorption as well as analysis of undesired simultaneous processes is crucially important in this regard. In this work, we have applied Molecular Dynamics (MD) to investigate the absorption of CO(2) from a binary mixture of CO(2) and CH(4) into aqueous piperazine activated MDEA solution. The MD simulations were performed at a constant temperature of 298 K for five different systems with a loading factor of 0.07 to provide insight into molecular distribution in the amine solution and to enhance understanding of absorption mechanisms on the molecular scale. Force field parameters that were missing from the OPLS-AA force field, as well as charge distribution of piperazine (PZ), protonated piperazine (PZH(+)), piperazine carbamate (PZCOO(-)) and MDEA were obtained by QM calculations. The results of our simulations emphasize the importance of piperazine and piperazine carbamate in accelerating the absorption process. For the first time, we have shown the undesirable trapping of CH(4) by the amine solution and revealed that amine groups are mainly responsible for both absorption of CO(2) and the undesired trapping of CH(4).     

Solvent and concentration effects on the visible spectra of tri-para-dialkylamino-substituted triarylmethane dyes in liquid solutions

We have characterized the spectroscopy properties of crystal violet (CV+) and ethyl violet (EV+) in liquid solutions as a function of the solvent type and dye concentration. The analysis of how solvent properties and dye concentration affects the electronic spectra of these tri-para-dialkylamino substituted tryarylmethane (TAM+) dyes was performed on the basis of two spectroscopic parameters, namely the difference in wavenumber (deltanu) between the maximum and the shoulder that appears in the short-wavelength side of the respective maximum visible band (deltanu = 1/lambda(shoulder)-1/lambda(max) cm(-1)), and the wavelength of the maximum absorption (lambda(max)). The solvent and the concentration effects on lambda(max) and deltanu have indicated that both solute/solute (ion-pairing and dye aggregation) and solute/solvent (H-bonding type) interactions modulate the shape of the visible electronic spectra of these dyes in solution. In solvent with small dieletric constant (epsilon < approximately 10), the formation of ion-pairs represents a major contribution to the shaping of these spectra. Upon increasing dye concentration the formation of ion-pairs was characterized by an increase in deltanu observed concomitantly with a red shift in lambda(max) In chloroform and chlorobenzene the ion-pair association constant of CV+ and EV+ with Cl- ions were found to be in the order of 10(6) and 10(5) M(-1), respectively. In trichloroethylene the association constant for the CV+Cl- pair was 10(8) M(-1). In water, dye aggregation instead of ion-pairing represents a major contribution to the shaping of the visible spectra of CV+ and EV+. Dye aggregation was indicated by an increase in deltanu observed concomitantly with a blue shift in lambda(max) upon increasing dye concentration. The distinct behavior of deltanu for dye aggregation and ion-pairing as a function of dye concentration can therefore assist in the characterization of these two distinct phenomena. The solute/solvent interactions were studied in a series of polar solvents in which solute/solute interactions do not occur in any detectable extent. The dependence found for deltanu as a function of the Kamlet-Tafts solvatochromic parameters (alpha, beta and pi*) is in keeping with previous inferences indicating that the splitting in the overlapped absorption band of CV+ and EV+ in hydroxilated solvents arises from a perturbation in the molecular symmetry induced by hydrogen bonding (donor-acceptor) type interactions with solvent molecules. A distinction between the effects of solute/solute and solute/solvent interactions on the visible spectra of these dyes is provided.     

Chemical Speciation and Bond Lengths of Organic Solutes by Core‐Level Spectroscopy: pH and Solvent Influence on p‐Aminobenzoic Acid

Through X‐ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near‐edge X‐ray absorption fine structure (NEXAFS) and resonant inelastic X‐ray scattering (RIXS) measurements at the nitrogen K‐edge of para‐aminobenzoic acid reveal both pH‐ and solvent‐dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.