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.     

Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection

End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.     

Single molecule photon emission statistics in the slow modulation limit

A framework for calculating photon emission statistics for single chromophores perturbed by slow environmental fluctuations is introduced. When internal chromophore dynamics are significantly faster than time scales for environmental modulation it becomes possible to invoke a type of adiabatic approximation, allowing for straightforward calculation of photon counting moments including explicitly quantum effects. Unlike previous exact treatments, the present methodology involves calculation of dynamics reflecting only the modulation characteristics of the environment and quantum dynamics of an isolated chromophore separately, i.e., the complicated intermingling of chromophore quantum dynamics and the environmental modulation are suppressed via the adiabatic approximation. This leads to significant conceptual and computational simplifications. Within its regime of applicability, the present approximation reproduces exact calculations quantitatively. We demonstrate this accuracy explicitly for the case of a two-level chromophore modulated by a number of different stochastic models.     

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.     

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald (PME) method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects.     

Theoretical procedure for optimizing dye-sensitized solar cells: from electronic structure to photovoltaic efficiency

A step-by-step theoretical protocol based on density functional theory (DFT) and time-dependent DFT at both the molecular and periodic levels is proposed for the design of dye-sensitized solar cell (DSSC) devices including dyes and electrolyte additives. This computational tool is tested with a fused polycyclic pyridinium derivative as a novel dye prototype. First, the UV-vis spectrum of this dye alone is computed, and then the electronic structure of the system with the dye adsorbed on an oxide semiconductor surface is evaluated. The influence of the electrolyte part of the DSSC is investigated by explicitly taking into account the electrolyte molecules co-adsorbed with the dye on the surface. We find that tert-butylpyridine (TBP) reduces the electron injection by a factor of 2, while lithium ion increases this injection by a factor of 2.4. Our stepwise protocol is successfully validated by experimental measurements, which establish that TBP divides the electronic injection by 1.6 whereas Li(+) multiplies this injection by 1.8. This procedure should be useful for molecular engineering in the field of DSSCs, not only as a complement to experimental approaches but also for improving them in terms of time and resource consumption.     

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.     

Solvent effects on NMR isotropic shielding constants. a comparison between explicit polarizable discrete and continuum approaches

The gas-to-aqueous solution shifts of the 17O and 13C NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.     

First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers

Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms.     

Self‐consistent field for fragmented quantum mechanical model of large molecular systems

Fragment‐based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter‐fragment electrostatic interactions, a dual‐layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual‐layer scheme, the self‐consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter‐fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter‐fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block‐wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.     

Recent Advances on Pt-Free Electro-Catalysts for Dye-Sensitized Solar Cells

Since Prof. Grätzel and co-workers achieved breakthrough progress on dye-sensitized solar cells (DSSCs) in 1991, DSSCs have been extensively investigated and wildly developed as a potential renewable power source in the last two decades due to their low cost, low energy-intensive processing, and high roll-to-roll compatibility. During this period, the highest efficiency recorded for DSSC under ideal solar light (AM 1.5G, 100 mW cm⁻²) has increased from ~7% to ~14.3%. For the practical use of solar cells, the performance of photovoltaic devices in several conditions with weak light irradiation (e.g., indoor) or various light incident angles are also an important item. Accordingly, DSSCs exhibit high competitiveness in solar cell markets because their performances are less affected by the light intensity and are less sensitive to the light incident angle. However, the most used catalyst in the counter electrode (CE) of a typical DSSC is platinum (Pt), which is an expensive noble metal and is rare on earth. To further reduce the cost of the fabrication of DSSCs on the industrial scale, it is better to develop Pt-free electro-catalysts for the CEs of DSSCs, such as transition metallic compounds, conducting polymers, carbonaceous materials, and their composites. In this article, we will provide a short review on the Pt-free electro-catalyst CEs of DSSCs with superior cell compared to Pt CEs; additionally, those selected reports were published within the past 5 years.     

Effects of Dye‐Adsorption Solvent on the Performances of the Dye‐Sensitized Solar Cells Based on Black Dye

The effects of the dye‐adsorption solvent on the performances of the dye‐sensitized solar cells (DSSCs) based on black dye have been investigated. The highest conversion efficiency (10.6 %) was obtained in the cases for which 1‐PrOH and the mixed solvent of EtOH and tBuOH (3:1 v/v) were employed as dye‐adsorption solvents. The optimized value for the dielectric constant of the dye‐adsorption solvent was found to be around 20. The DSSCs that used MeOH as a dye‐adsorption solvent showed inferior solar‐cell performance relative to the DSSCs that used EtOH, 1‐PrOH, 2‐PrOH, and 1‐BuOH. Photo‐ and electrochemical measurements of black dye both in solution and adsorbed onto the TiO₂ surface revealed that black dye aggregates at the TiO₂ surface during the adsorption process in the case for MeOH. Both the shorter electron lifetime in the TiO₂ photoelectrode and the greater resistance in the TiO₂–dye–elecrolyte interface, attributed to the dye aggregation at the TiO₂ surface, cause the decrease in the solar‐cell performance of the DSSC that used MeOH as a dye adsorption solvent.     

Sensitizers for Aqueous‐Based Solar Cells

Aqueous dye‐sensitized solar cells (DSSCs) are attractive due to their sustainability, the use of water as a safe solvent for the redox mediators, and their possible applications in photoelectrochemical water splitting. However, the higher tendency of dye leaching by water and the lower wettability of dye molecules are two major obstacles that need to be tackled for future applications of aqueous DSSCs. Sensitizers designed for aqueous DSSCs are discussed based on their functions, such as modification of the molecular skeleton and the anchoring group for better stability against dye leaching by water, and the incorporation of hydrophilic entities into the dye molecule or the addition of a surfactant to the system to increase the wettability of the dye for more facile dye regeneration. Surface treatment of the photoanode to deter dye leaching or improve the wettability of the dye molecule is also discussed. Redox mediators designed for aqueous DSSCs are also discussed. The review also includes quantum‐dot‐sensitized solar cells, with a focus on improvements in QD loading and suppression of interfacial charge recombination at the photoanode.     

Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE)

Characterization of the conformational ensemble of disordered proteins is highly important for understanding protein folding and aggregation mechanisms, but remains a computational and experimental challenge owing to the dynamic nature of these proteins. New observables that can provide unique insights into transient residual structures in disordered proteins are needed. Here using denatured ubiquitin as a model system, NMR solvent paramagnetic relaxation enhancement (sPRE) measurements provide an accurate and highly sensitive probe for detecting low populations of residual structure in a disordered protein. Furthermore, a new ensemble calculation approach based on sPRE restraints in conjunction with residual dipolar couplings (RDCs) and small‐angle X‐ray scattering (SAXS) is used to define the conformational ensemble of disordered proteins at atomic resolution. The approach presented should be applicable to a wide range of dynamic macromolecules.     

Quantum simulation of solution phase intramolecular electron transfer rates in betaine-30

Mixed quantum-classical atomistic simulations have been carried out to investigate the mechanistic details of excited state intramolecular electron transfer in a betaine-30 molecule in acetonitrile. The key electronic degrees of freedom of the solute molecule are treated quantum mechanically using the semiempirical Pariser-Parr-Pople Hamiltonian, including the solvent influence on electronic structure. The intramolecular vibrational modes are also treated explicitly at a quantum level, with the remaining elements treated classically using empirical potentials. The electron-transfer rate, corresponding to S1 --> S0 relaxation, is evaluated via time-dependent perturbation theory with the explicit inclusion of the dynamics of solvation and intramolecular conformation. The calculations reveal that, while solvation dynamics is critical to the rate, the intramolecular torsional dynamics also plays an important role. The importance of the use of multiple high-frequency quantum modes is also discussed.