Explicit Solute-solvent Interactions Research Articles

Absorption and fluorescence spectra of new pyrrolo[3,4‐b]quinolizines in condensed phases: A joint experimental and computational study

AbstractNewly synthesized pyrrolo[3,4‐b]quinolizines, blue‐green to orange‐red in fluorescent dye in solutions and yellow to red fluorescent dyes in solid states, were experimentally and computationally investigated for the electronic and fluorescence spectra in solution as well as in solid state. The solvent effects on the absorption and emission spectra were theoretically investigated by the snapshots‐averaged spectra obtained by the first principle molecular dynamics combined with polarizable continuum model (PCM). Alternatively, the solute–solvent interaction effect on the spectra was examined by fragment molecular orbital‐time dependent density functional theory (FMO‐TDDFT) which considered the explicit solute–solvent interactions. The results indicate that the quantitative prediction limitations of PCM and that the solvatochromic shifts in dichloromethane and ethanol were correctly reproduced by FMO‐TDDFT. The luminescence quantum yields of the compounds were analyzed on the excited state potential surface via the S0/S1‐conical intersections.

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.

Comprehensive Experimental and Computational Spectroscopic Study of Hexacyanoferrate Complexes in Water: From Infrared to X-ray Wavelengths.

We present a joint experimental and computational study of the hexacyanoferrate aqueous complexes at equilibrium in the 250 meV to 7.15 keV regime. The experiments and the computations include the vibrational spectroscopy of the cyanide ligands, the valence electronic absorption spectra, and Fe 1s core hole spectra using element-specific-resonant X-ray absorption and emission techniques. Density functional theory-based quantum mechanics/molecular mechanics molecular dynamics simulations are performed to generate explicit solute-solvent configurations, which serve as inputs for the spectroscopy calculations of the experiments spanning the IR to X-ray wavelengths. The spectroscopy simulations are performed at the same level of theory across this large energy window, which allows for a systematic comparison of the effects of explicit solute-solvent interactions in the vibrational, valence electronic, and core-level spectra of hexacyanoferrate complexes in water. Although the spectroscopy of hexacyanoferrate complexes in solution has been the subject of several studies, most of the previous works have focused on a narrow energy window and have not accounted for explicit solute-solvent interactions in their spectroscopy simulations. In this work, we focus our analysis on identifying how the local solvation environment around the hexacyanoferrate complexes influences the intensity and line shape of specific spectroscopic features in the UV/vis, X-ray absorption, and valence-to-core X-ray emission spectra. The identification of these features and their relationship to solute-solvent interactions is important because hexacyanoferrate complexes serve as model systems for understanding the photochemistry and photophysics of a large class of Fe(II) and Fe(III) complexes in solution.

Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water.

We have proposed a new theoretical methodology to clarify the microscopic nature of the vibrational properties in solution, which consists of a combination of the vibrational frequency analyses (VFAs) with two kinds of Hessian matrices, that is, the effective Hessian on the free energy surface (free energy Hessian: "FE-Hessian") and the instantaneous one (instantaneous normal mode Hessian: "INM-Hessian") within QM/MM framework. In these VFAs, the Hessians were obtained by the analytical approach, having the advantages from the aspect of both the computational efficiency and accuracy in comparison to those obtained by the numerical one. In the present study, we have applied them to the glycine aqueous solution. First, by using the VFA with the FE-Hessian (VFA-FEH), we estimated the vibrational frequency shifts induced by solvent water molecules. The calculated values were quantitatively in agreement with experimental ones. It was clearly demonstrated that such vibrational shifts are attributed to not only the structural relaxation but also the explicit solute-solvent interactions (i.e., interatomic interactions). Second, by using the VFA with the INM-Hessian (VFA-INMH), the vibrational spectra in solution were investigated through the vibrational INM densities of states (DOS). By the comparison between the spectroscopic features and the microscopic solvation structure around glycine molecule, it was found that the frequency shifts and bandwidths in IR spectra are closely correlated with the hydrogen bonding (HB) network formations. In particular, the instantaneous changes of vibrational states of the hydroxyl group and carbonyl one, showing apparently inverse tendency on the strength of the HB interaction, can be explained very well on the basis of two different mechanisms, that is, the direct change of electron density in the bonding orbitals and the indirect one due to hyperconjugation between the lone electron pair and the antibonding orbitals, respectively. In conclusion, the present dual VFA approach is a quite useful strategy to interpret the microscopic origin of the experimental vibrational spectra.

Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions.

Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable.

Structure of a uranyl peroxo complex in aqueous solution from first-principles molecular dynamics simulations

Static ab initio and density-functional computations, as well as Car-Parrinello molecular dynamics simulations in aqueous solution are reported for [UO2(OH)(κ(2)-O2)(H2O)2](-) and [UO2(OH)2(κ(1)-O2H)(H2O)](-). Whereas the κ(1)-hydroperoxo isomer is found to be more stable than the κ(2)-peroxo form in the gas phase, the order of stability is reversed in explicit bulk solution. Based on free energies from thermodynamic integration (BLYP functional), the peroxo form is favoured by ca. 32 kJ mol(-1) in water. This stabilisation is discussed in terms of the hydration shells about the individual ligands and dipole moments of the complexes in water, and highlights the importance of explicit solute-solvent interactions and bulk solvation for the speciation of uranyl(vi) compounds.

The Effect of Explicit Solvent on Photodegradation of Decabromodiphenyl Ether in Toluene: Insights from Theoretical Study

Polybrominated diphenyl ethers (PBDEs) have received special environmental concern because of their potential toxicity to humans and wildlife worldwide. However, their photochemical degradation mechanisms remain largely unknown. Herein, a PCM/TD-DFT scheme (time-dependent density functional theory combined with the polarizable continuum model) augmented with explicit solute-solvent interactions is used to explore the promotive effects of the toluene solvent on the photochemical degradation debromination of deca-BDE (BDE209). The face-to-face π-π interactions between penta-bromine-substituted phenyl and toluene are investigated. The calculations indicate that the face-to-face π-π interaction plays an important role in the low-lying π→σ* transitions of BDE209-toluene π-stacking complex at around 300 nm in the sunlight region, which leads to notable changes for the πσ* excited states and which promotes the breaking of the C-Br bonds. The photodegradation reaction via an intermolecular charge-transfer excited state formed by the electronic transition from a π orbital of toluene to a σ* orbital of BDE209 is found to be a dominant mechanism. Our calculation results reveal the mechanism of how the participation of an explicit toluene solvent molecule catalyzes the photodegradation of BDE209 and explain the experimental results successfully. The present study may provide helpful information for the removal of PBDE contamination.

Mechanisms for Solvatochromic Shifts of Free-Base Porphine Studied with Polarizable Continuum Models and Explicit Solute-Solvent Interactions.

Solvatochromic shifts of free-base porphine in the Q-band and B-band were studied using the polarizable continuum model (PCM) and explicit solvent molecules employing time-dependent density functional theory (TDDFT) and the symmetry-adapted cluster-configuration interaction (SAC-CI) method. The state-specific (SS) and linear-response (LR) methods were examined in the PCM calculations. These models involve different types of solute-solvent interactions. The LR PCM and explicit solvation models reproduced the experimentally observed trends of the solvatochromic shifts, while the SS PCM failed to reproduce the experimental findings. The origin of the solvatochromic shifts of free-base porphine was dispersive interactions between the solute and solvent. Specific solute-solvent interactions would be important for a decrease of the splitting width between Q-bands. Based on the Casimir-Polder formula and a decomposition analysis, it was found that the dominant part of the solute-solvent interactions can be considered using independent particle approximations.

Characterizing Aqueous Solution Conformations of a Peptide Backbone Using Raman Optical Activity Computations

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N′-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (αR) and left-handed (αL) helical conformations. The computed ROA spectra based on MC-sampled αR and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the αL- and β-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the αR and PPII conformations but no substantial population of αL- or β-structures, despite sampling αL- and β-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.

A study of peculiar tautomerism of pyrido62,3-c961,2,69thiadiazine 2,2-dioxide system

A systematic study of the tautomerism of 4-amino-1 H -pyrido[2,3- c ][1,2,6]thiadiazine 2,2-dioxide has been carried out. Thus, the relativity stability of the possible tautomers has been studied in the gas phase by ab initio and functional density theory (DFT) methods. The theoretical study in solution has been carried out using several continuum solvation models as self consistent reaction field (SCRF) and the Poisson-Boltzmann method. In addition, complexes with one or two molecules of water have been calculated in order to consider explicit solute–solvent interactions. These results have been compared with UV spectrophotometry data, giving good agreement between theoretical and experimental results in aqueous solution. Finally, the gauge invariant atomic orbital method (GIAO) for calculating magnetic absolute shielding with both the ab initio method (RHF/6-31G*) and density functional theory (B3LYP/6-31G*) have been applied to explore this method to study the tautomeric equilibrium in the pyrido[2,3- c ][1,2,6]thiadiazine 2,2-dioxide system.

A study of peculiar tautomerism of pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide system

A systematic study of the tautomerism of 4-amino-1 H-pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide has been carried out. Thus, the relativity stability of the possible tautomers has been studied in the gas phase by ab initio and functional density theory (DFT) methods. The theoretical study in solution has been carried out using several continuum solvation models as self consistent reaction field (SCRF) and the Poisson-Boltzmann method. In addition, complexes with one or two molecules of water have been calculated in order to consider explicit solute–solvent interactions. These results have been compared with UV spectrophotometry data, giving good agreement between theoretical and experimental results in aqueous solution. Finally, the gauge invariant atomic orbital method (GIAO) for calculating magnetic absolute shielding with both the ab initio method (RHF/6-31G*) and density functional theory (B3LYP/6-31G*) have been applied to explore this method to study the tautomeric equilibrium in the pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide system.

Solvent effects on the internal rotation of neutral and protonated glyoxal

Torsional energy profiles for internal rotation of the CHO group in glyxxal and protonated glyoxal have been studied both in gas phase and aqueous solution at the MP2/6-31G(d) level. The effect of solvation on the basic features of the internal rotation profiles has been accounted for by using a discrete-continuum supermolecule Polarizable Continuum Model (PCM) representation of the solvent. For protonated glyoxal, a more detailed analysis has been conducted, studying the whole rotational potential energy surface generated as a function of the CC bond rotation and proton cis-trans isomerism coordinates. Additional single point iterative MRCI calculations were performed using the CIPSI program to assess the quality of the one-configuration representation. The effect of solvation on the structural parameters and relative energies is thoroughly analyzed for each of the systems under study, with particular attention addressed to correctly ascribe the role of explicit solute-solvent interactions together with macroscopic solvent effects. In order to predict free energies in solution at 298 K, zero point energy and thermal corrections have also been calculated at the same level of theory for all the stationary points here characterized.