The authors thank Prof. David Coker for useful discussions and Science Foundation Ireland (SFI) for the provision of High-Performance Computing resources. This research has been supported by the SFI-NSFC bilateral funding scheme (grant number SFI/17/NSFC/5229), as well as the Programme for Research in Third Level Institutions (PRTLI) Cycle 5, co-funded by the European Regional Development Fund.

1. Performing MD Simulation using DL_POLY
<ol>
	<li>Construct the DSC-systems initial structure of the N719-dye adsorbed to an anatase-titania (101) surface solvated by [bmim]+[NTf2]- taken from previous work12,13. Draw the required structure using VESTA software.</li>
	<li>Choose the N719 cis-di(thiocyanato)-bis (2,2&#39;-bipyridl-4-carboxylate-4&#39;-carboxylic acid)-ruthenium (II)-sensitizing dye with no counterions and ensure the presence of two surface-bound protons to provide for overall-system charge neutrality. 
	NOTE: Indeed, in depth studies by De Angelis et al. have established this to constitute a realistic representation of N719 adsorbed to anatase-titania21. This is because in ref. 21, there was the most convincing level of agreement with experimental results for a number of properties; in experimental systems, the de-facto surface protonation is thought to emerge from ILs&#39; cations and anions leading to some degree of charge transfer with the surface21.</li>
	<li>Ensure that the dye is adsorbed chemically to the TiO2 surface through two carboxylate groups (i.e., bidentate). This initial adsorbed dye configuration is similar to that denoted as I1 and found by Schiffman et al.22, which was determined to be the most stable with surface protonation taken into account. Consult refs. 12 &#38; 13 for a detailed account of how this is done, including chemical-adsorption coordinates.</li>
	<li>Ensure that the sensitizing dye N719 (cis-di(thiocyanato)-bis(2,20-bipyridl-4-carboxylate-40-carboxylic acid)-ruthenium(II)) has no counterions. Add two surface-bound protons for charge neutrality, as in ref. 12 &#38; 13.</li>
	<li>Select 12 cation-anion pairs of 1-butyl-3 methylimidazolium bis(trifluoromethyl sulfonyl)imide, comprising 480 atoms12,13. These were taken from refs. 12 &#38; 13.</li>
	<li>Relax the RTIL configuration via empirical-potentials, using the well-validated forcefield of Lopes et al.23. Model anatase using the Matsui-Akaogi (MA) force-field and include the mobility of the titania in the relaxation process. Using the DL-POLY details in step 2.1 below, perform a geometry-optimization in DL-POLY, rather than MD, with a conjugate-gradient-minimization relative termination gradient of 0.001. Here, specify optimization in the FIELD file, rather than dynamics.</li>
	<li>For the anatase surface, (TiO2)96, consisting of 288 atoms, ensure it is periodic along x- and y- laboratory axes, projecting to the RTIL a pair of parallel (101) surfaces; the dimensions in x-axis 23 &#197; and y-axis to 21 &#197;. This was taken from refs. 12 &#38; 13.</li>
	<li>Ensure that the entire DSC system with an explicit solvent is composed of 827 atoms12,13; For the &#39;in-vacuo&#39; case, bereft of RTIL solvation, there should be 347 atoms in the system.</li>
</ol>
2. Performing forcefield-based MD Simulation using DL_POLY
<ol>
	<li>Perform MD using DL-POLY with various different partial-charge sets (vide infra) for 15 ps with a 1 fs time-step and at 300 K in an NVT ensemble24,25, using the Lopes et al.23 forcefield parameters for the RTIL and general-purpose OPLS model for the dye26, with the well-studied and reliable Matsui-Akaogi potential acting for titania27 force-field. To run DL-POLY on the terminal, type DLPOLY.X &#38; where the input files are located.</li>
	<li>Perform classical MD via these above-specified empirical force-fields, as implemented in DL_POLY28. Here, there is no need to use a graphical user interface (GUI) in the software, so it is recommended to input the details using the comprehensive, and easy-to-follow software manual29. Here, in the CONTROL file (check Supplemental Information for the input files), specify &#39;Nose-Hoover&#39; for NVT, and opt for position-velocity trajectory printing every 1 fs.</li>
	<li>In the FIELD file, for Lennard-Jones parameters, apply Lorentz-Berthelot combining rules25. Taking the arithmetic mean of the Lennard-Jones (LJ) radii and the geometric mean of the LJ well-depths, for the empirical force-fields, as detailed in ref. 25, and enter this in the bottom section of the FIELD file under the non-bonded-interactions tab.</li>
	<li>To handle long-range electrostatics, apply the Ewald method25; use a non-bonded cut-off length of rcut = 10 &#197;. Consult refs. 25 &#38; 30 for precise details as to how to optimize electrostatic parameters. Set the real-space decay parameter for the Ewald method in the CONTROL file to be ~3.14/rcut, and choose the number of Ewald wave-vectors to ensure a relative tolerance in the Ewald evaluation of 1E-5; specify that in the CONTROL file.</li>
	<li>Ensure, in the CONTROL file, state that rcut = 10 &#197;; carry out a series of potential-energy evaluations with a REVCON file (renamed as CONFIG) until the system pressure in OUTPUT converges to within a few percent to choose rcut, but avoid any rcut below ~2.5 times the largest LJ distance25,30. 
	NOTE: This short 15 ps MD-propagation timescale is chosen to be similar to that of ~8.5 ps Born-Oppenheimer-MD (BOMD) simulations with an identical starting configuration of refs. 9, 10 &#38; 17, so as to allow for direct comparison vibrational-spectra prediction afforded by both AI-20 and forcefield-based MD (with comparison and validation against experiment also).</li>
	<li>From the HISTORY file (into which both velocities and positions have been printed at each time step, as directed from the CONTROL file), extract the x-, y-, z-velocities by using python dye_atom_velocity_seperate.py (see Supplemental Information) in the terminal. It will separate the velocities at each step.</li>
	<li>Compute the VACF by using vacf151005.py (see Supplemental Information). In the terminal, type ./classical_dye_autocorr.sh; it will compute the VACF of all dye atoms. Compute spectra from MD (whether AIMD14,20 or forcefield-based) using mass-weighted Fourier transforms of the dye&#39;s atomic velocity autocorrelation function (VACF)31,32,33 by using python MWPS.py (see Supplemental Information). In the terminal, type ./run_all_4.sh; it will compute the mass weighted power spectra.</li>
	<li>Perform a Fourier transform on these VACFs using commonly available software.</li>
	<li>Bear in mind that the best-quality DFT treatment in AIMD (e.g., use of explicit solvation and accurate treatment of dispersion, alongside a canny choice of functional) is important to use for benchmarking against experimental data12,13,20 and gauging/tailoring the comparative performance of empirical-potential MD, in particular, the large influence of electrostatics and choices for partial charges16. See refs. 12 and 13 and study these to gain an in-depth appreciation, and, if intending to do AIMD (which is not the case in the present study), act accordingly in such a situation in the future, should the need to conduct AIMD arise.</li>
</ol>
3. Comparing results of each of the force-fields
NOTE: It is important to assess partial-charge sets for the RTIL for empirical-potential-based MD simulation in step 2, for ready comparison against each other, experiment and ab initio-MD results in explicit RTIL solvent (using the PBE functional with Grimme-D3 dispersion, given its superior performance for prediction of vibrational spectra)20; these were as follows:
<ol>
	<li>Note that in the case of literature-derived RTIL charges, the anion charges are to be found from Extended H&#252;ckel Theory34,35, based on AIMD trajectories23, owing to the absence of anion-charge parameterisation in ref. 20, with cation charges to be taken from Lopes et al.23 Prepare a table of the literature charges, and put into FIELD-file format for DL-POLY.</li>
	<li>Note that Mulliken RTIL charges are to be calculated via Mulliken population analysis. Perform the Mulliken analysis by averaging over four points of the ab initio MD trajectory20, renormalize and prepare a table of the literature charges, and put into FIELD-file format for DL-POLY.</li>
	<li>Note that Extended H&#252;ckel Theory (EHT) charges are to be fitted from the final configuration of AIMD trajectories20, using EHT, applied to both RTIL anions and cations. Perform the EHT analysis by averaging over four points of the ab initio MD trajectory20, as implemented in the MOE software package (by selecting &#39;Charge Analysis&#39; menu after reading in the configuration file)35, renormalize and prepare a table of the literature charges, and put into FIELD-file format for DL-POLY.</li>
	<li>Note that Hirshfeld RTIL charges are to be calculated from Hirshfeld-charge analysis by averaging over four points of the ab initio MD trajectory20, for anions and cations20, as implemented in the MOE software package (by selecting &#39;Charge Analysis&#39; menu after reading in the configuration file)35. From renormalization of these so-obtained charges, tabulate these in the appropriate format in the DL-POLY FIELD file.</li>
	<li>Bear in mind that the different charge sets for the [bmim]+[NTf2]- atoms are presented in Table 1 &#38; Table 2, which also show the mean amount by which some of the atomic charges needed to be modified, so as to take symmetry and overall charge conservation into account.</li>
	<li>Note that the final charge sets are to have the sum of charges adding up to +1 on the cation and -1 on the anion. The cation and anion are shown in Figure 1a and Figure 1b, respectively. The underlying DFT-sampled spectra, from which these charge sets were inspired, by and large, have implicit charge transfer and tend to lead to charges closer to &#177;1.</li>
</ol>

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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vibrational+spectroscopic+study+of+the+coordination+of+(2,+2'-bipyridyl-4,+4'-dicarboxylic+acid)+ruthenium+(II)+complexes+to+the+surface+of+nanocrystalline+titania.">Vibrational spectroscopic study of the coordination of (2, 2'-bipyridyl-4, 4'-dicarboxylic acid) ruthenium (II) complexes to the surface of nanocrystalline titania.</a> Langmuir. 14, 2744-2749 (1998).</li><li>Le&#243;n, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Vibrational Spectroscopy of Photosensitizer Dyes for Organic Solar Cells. , (2006).</li></ol>

The authors have nothing to disclose.

Ab initio simulation techniques are expensive to perform and hence to perform simulation on much longer timescales would require the use of empirical forcefields for at least some of the DSC system. Towards this end, an equivalent atomistic model was created of the [bmim]+[NTf2]- solvated interface, using an empirical, classical-simulation forcefield for MD. The anatase was modeled using the Matsui-Akaogi (MA) forcefield, whilst the dye structure was handled using OPLS parameters. For the RTIL, four...

In dye-sensitized solar cells (DSCs), the optical band gap of semiconductors is bridged by a light-absorbing, or sensitizing, dye. DSCs require continual recharging: therefore, a redox electrolyte is essential to foster this constant supply of charge (typically in the form of an I-/I3-, in an organic solvent). This facilitates the passage of holes from the sensitizing dye to the electrolyte, with injected photo-excited electrons into the metal-oxide substrate passing through to an external circuit, with eventual recombination taking place at the cathode1. A crucial aspect underpinning DSCs&#39; positive outlook for a wide variety of real world applications originates in their straightforward manufacture, without the need for raw materials high in purity; this is in stark contrast with the high capital cost and ultra-purity required for silicon-based photovoltaics. In any event, the prospect of significantly improving the working-life timescales of DSCs by swapping less stable electrolytes with room-temperature ionic liquids (RTILs) having low volatility shows significant promise. The solid-like physical properties of RTILs combined with their liquid-like electrical properties (such as low toxicity, flammability, and volatility)1 lead these to constitute rather excellent candidate electrolytes for usage in DSC applications.
Given such prospects for RTILs in DSCs, it is hardly surprising that, in recent years, there has been a substantial boost of activity in studying DSC-prototype N719-chromophore/titania interfaces with RTILs. In particular, important work on such systems has been performed2,3,4,5, which consider a broad suite of physico-chemical processes, including the charge-replenishment kinetics in dyes2,5, the mechanistic steps of electron-hole dynamics and transfer3, and, of course, the effects of titania substrates&#39; nanoscale nature upon these, and other, processes4.
Now, bearing in mind impressive advances in DFT-based molecular simulation, particularly AIMD6, as a highly useful prototypical design tool in materials science and particularly for DSCs7,8,9,10,11, with critical assessment of optimal functional selection being vital8,9, AIMD techniques have proven very useful previously in scrutinizing rather significant dispersion and explicit-RTIL solvation effects on dye structure, adsorption modes and vibrational properties at DSC-semiconductor surfaces. In particular, the adoption of AIMD had led to some success in attaining reasonable, semi-quantitative capture and prediction of important electronic properties, such as band gap, as well as structural binding13 and vibrational spectra14 In refs. 12-14, AIMD simulations were performed extensively on the photo-active N719-chromophore dye bound to (101) anatase-titania surface, assessing both electronic properties and structural properties in the presence of both [bmim]+[NTf2]- 12,13 and [bmim]+[I]- 14 RTILs, in addition to vibrational spectra for the case of [bmim]+[I]- 14. In particular, the rigidity of the semiconductor&#39;s surface15, apart from its inherent comparative photo-activity, led the surface to slightly alter within the AIMD simulation, which makes (101) anatase interfaces12,13,14 a suitable choice. As ref. 12 shows, the mean distance between the cations and the surface dropped by about 0.5 &#197;, the average separation between the cations and anions decreased by 0.6 &#197;, and the noticeable altering of the RTILs in the first layer around the dye, where the cation was on average 1.5 &#197; further from the center of the dye, were directly caused by explicit dispersion interactions in RTIL-solvated systems. Unphysical kinking of the adsorbed N719 dye&#39;s configuration was also a result of the introduction of explicit dispersion effects in vacuo. In ref. 13, analysis was conducted on whether these structural effects of explicit RTIL solvation and functional selection affected the behavior of the DSSCs, concluding that both explicit solvation and treatment of dispersion is very important. In ref. 14, with high-quality experimental vibrational-spectral data of other groups on hand, the particular effects were benchmarked systematically on both explicit [bmim]+[I]- solvation and accurate handling of dispersion established in refs. 12 &#38; 13 on the reproduction of salient spectral-mode features; this led to the conclusion that explicit solvation is important, alongside accurate treatment of dispersion interactions, echoing earlier findings for both structural and dynamical properties in the case of AIMD modeling of catalysts in explicit solvent16. Indeed, Mosconi et al. have also performed an impressive assessment of explicit-solvation effects on DFT treatment of DSC simulation17. Bahers et al.18 studied experimental absorption spectra for dyes along with the related spectra at the TD-DFT level; these TD-DFT spectra agreed very well in terms of their computed transitions with their experimental counterparts. In addition, absorption spectra of pyrrolidine (PYR) derivatives were studied by Preat et al. in several solvents19, providing significant insights into the dyes&#39; geometrical and electronic structures, and evincing adequate structural modifications that serve to optimize the properties of the PYR-based DSSCs - a spirit of simulation-led/rationalized &#39;molecular design&#39;, indeed.
Having clearly established the important contribution of both DFT and AIMD towards accurate modelling of DSCs&#39; properties and function, including such important technical matters like explicit solvation and appropriate treatment of dispersion interactions from structural, electronic and vibrational standpoints7,8,9,10,11,12,13,14, now - in the present work - the focus turns towards the pragmatic question of how well empirical-potential approaches can be tailored to address the apposite and reasonable prediction of structural and vibrational properties of such prototypical DSC systems, taking the N719 dye adsorbed on anatase (101) in the [bmim]+[NTf2]- RTIL as a case in point. This is important, not only because of the large corpus of forcefield-based molecular-simulation activities and methodological machinery available to tackle DSC simulation7, and metal-oxide surfaces more widely, but also because of their staggeringly reduced computational cost vis-&#224;-vis DFT-based approaches, together with the possibility of very efficient coupling to biased-sampling approaches to capture more efficiently phase space and structural evolution in highly viscous RTIL solvents, dominated by solid-like physical properties at ambient temperatures. Therefore, motivated by this open question of gauging and optimizing forcefield approaches, informed by both DFT and AIMD as well as experimental data for vibrational spectra14, we turn to the pressing task of assessing empirical-potential performance at vibrational-spectra prediction from MD, using mass-weighted Fourier transforms of the N719 dye&#39;s atomic velocity autocorrelation function (VACF). One key concern is how different partial-charge parameterizations of the RTIL may affect vibrational-spectra prediction, and particular attention was given to this point, as well as the wider task of tailoring forcefields for optimal spectral-mode prediction relative to experiment and AIMD20.

<table><tbody><tr><td>This was a molecular simulation, so no experimental equipment was used.</td><td></td><td></td><td></td></tr><tr><td>The name of the software was DL-POLY (the &#039;Classic&#039; version of which is available under GnuPublic Licence, via sourceforge)</td><td></td><td></td><td></td></tr></tbody></table>

vibrational spectra of a n719-chromophore/titania interface from empirical-potential molecular-dynamics simulation, solvated by a room temperature ionic liquid

The accurate molecular simulation prediction of vibrational spectra, and other structural, energetic and spectral characteristics, of photo-active metal-oxide surfaces in contact with light-absorbing dyes is an ongoing thorny and elusive challenge in physical chemistry. With this in mind, a molecular-dynamics (MD) simulation were performed by using optimized empirical potentials for a well-representative and prototypical dye-sensitized solar cell (DSC) solvated by a widely-studied room temperature ionic liquid (RTIL), in the guise of a [bmim]+[NTf2]- RTIL solvating an N719-sensitizing dye adsorbed onto 101 anatase-titania. In doing so, important insights were gleaned into how using a RTIL as the electrolytic hole acceptor modulates the dynamical and vibrational properties of a N719 dye, estimating the spectra for the DSC photo-active interface via Fourier transformation of mass-weighted velocity autocorrelation functions from MD. The acquired vibrational spectra were compared with the experiment spectra and those sampled from ab initio molecular dynamics (AIMD); in particular, various empirical-potential spectra generated from MD provide insight into how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction. In any event, careful fitting of empirical force-field models has been shown to be an effective tool in handling DSC vibrational properties, when validated by AIMD and an experiment.

Structural Properties of Binding Motifs 
Representative binding motifs for the four different partial-charge sets are depicted in Figure 2, after 15 ps of MD. In Figure 2a, for the (above-described) literature-derived charges, it can be seen that there is a prominent hydrogen-bonding interaction with a surface proton. From careful analyses of the trajectory, the hydrogen bonds are mostly sur...

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Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.

The accurate molecular simulation prediction of vibrational spectra, and other structural, energetic and spectral characteristics, of photo-active ...

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5.6K Views.  University College Dublin, Belfield. Dit protocol behandelt hoe goed empirische potentiële benaderingen kunnen worden aangepast aan de en redelijke voorspelling van structurele en trillingseigenschappen van prototypische kleurstof-gesensibiliseerde zonnecelsystemen aan te pakken. Dit is belangrijk vanwege de onthutsend verminderde computationele kosten benaderingen met de mogelijkheid van verschillende bemonstering benaderingen. Om een moleculair dynamische simulatie uit te voeren, opent u het DL_POLY simulatiesoftwarebestand e...

Video: Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding

Herein, we demonstrate that a bottom-up approach, based on halogen bonding (XB), can be successfully applied for the design of a new type of ionic liquid crystals (ILCs). Taking advantages of the high specificity of XB for haloperfluorocarbons and the ability of anions to act as XB-acceptors, we obtained supramolecular complexes based on 1-alkyl-3-methylimidazolium iodides and iodoperfluorocarbons, overcoming the well-known immiscibility between hydrocarbons (HCs) and perfluorocarbons (PFCs). The high directionality of the XB combined with the fluorophobic effect, allowed us to obtain enantiotropic liquid crystals where a rigid, non-aromatic, XB supramolecular anion acts as mesogenic core.
X-ray structure analysis of the complex between 1-ethyl-3-methylimidazolium iodide and iodoperfluorooctane showed the presence of a layered structure, which is a manifestation of the well-known tendency to segregation of perfluoroalkyl chains. This is consistent with the observation of smectic mesophases. Moreover, all the reported complexes melt below 100 &#176;C, and most are mesomorphic even at room temperature, despite that the starting materials were non-mesomorphic in nature.
The supramolecular strategy reported here provides new design principles for mesogen design allowing a totally new class of functional materials.

A protocol for the synthesis of a new type of mesogens, based on the halogen-bonded supramolecular anion [CnF2n+1-I&#183;&#183;&#183;I&#183;&#183;&#183;I-CnF2n+1]&#8722;, is reported.

Herein, we demonstrate that a bottom-up approach, based on halogen bonding (XB), can be successfully applied for the design of a new type of ionic liquid ...

Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy

As a second-order nonlinear optical spectroscopy, sum frequency generation (SFG) vibrational spectroscopy has widely been used in investigating various surfaces and interfaces. This non-invasive optical technique can provide the local molecular-level information with monolayer or submonolayer sensitivity. We here are providing experimental methodology on how to selectively detect the buried interface for both macromolecules and biomacromolecules. With this in mind, interfacial secondary structures of silk fibroin and water structures around model short-chain oligonucleotide duplex are discussed. The former shows a chain-chain overlap or spatial confinement effect and the latter shows a protection function against the Ca2+ ions resulting from the chiral spine superstructure of water.

Being comprehensively utilized, sum frequency generation (SFG) vibrational spectroscopy can help to reveal chain conformational order and secondary structural change happening at polymer and biomacromolecule interfaces.

As a second-order nonlinear optical spectroscopy, sum frequency generation (SFG) vibrational spectroscopy has widely been used in investigating various ...

Biochemistry

Total Internal Reflection Absorption Spectroscopy (TIRAS) for the Detection of Solvated Electrons at a Plasma-liquid Interface

The total internal reflection absorption spectroscopy (TIRAS) method presented in this article uses an inexpensive diode laser to detect solvated electrons produced by a low-temperature plasma in contact with an aqueous solution. Solvated electrons are powerful reducing agents, and it has been postulated that they play an important role in the interfacial chemistry between a gaseous plasma or discharge and a conductive liquid. However, due to the high local concentrations of reactive species at the interface, they have a short average lifetime (~1 &#181;s), which makes them extremely difficult to detect. The TIRAS technique uses a unique total internal reflection geometry combined with amplitude-modulated lock-in amplification to distinguish solvated electrons&#39; absorbance signal from other spurious noise sources. This enables the in situ detection of short-lived intermediates in the interfacial region, as opposed to the bulk measurement of stable products in the solution. This approach is especially attractive for the field of plasma electrochemistry, where much of the important chemistry is driven by short-lived free radicals. This experimental method has been used to analyze the reduction of nitrite (NO2-(aq)), nitrate (NO3-(aq)), hydrogen peroxide (H2O2(aq)), and dissolved carbon dioxide (CO2(aq)) by plasma-solvated electrons and deduce effective rate constants. Limitations of the method may arise in the presence of unintended parallel reactions, such as air contamination in the plasma, and absorbance measurements may also be hindered by the precipitation of reduced electrochemical products. Overall, the TIRAS method can be a powerful tool for studying the plasma-liquid interface, but its effectiveness depends on the particular system and reaction chemistry under study.

Total Internal Reflection Absorption Spectroscopy TIRAS for the Detection of Solvated Electrons at a Plasma-liquid Interface

This article presents a total internal reflection absorption spectroscopy (TIRAS) method for measuring short-lived free radicals at a plasma-liquid interface. In particular, TIRAS is used to identify solvated electrons based on their optical absorbance of red light near 700 nm.

The total internal reflection absorption spectroscopy (TIRAS) method presented in this article uses an inexpensive diode laser to detect solvated ...

Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals

We discuss in this article the experimental measurements of the molecules in liquid crystal (LC) phase using the time-resolved infrared (IR) vibrational spectroscopy and time-resolved electron diffraction. Liquid crystal phase is an important state of matter that exists between the solid and liquid phases and it is common in natural systems as well as in organic electronics. Liquid crystals are orientationally ordered but loosely packed, and therefore, the internal conformations and alignments of the molecular components of LCs can be modified by external stimuli. Although advanced time-resolved diffraction techniques have revealed picosecond-scale molecular dynamics of single crystals and polycrystals, direct observations of packing structures and ultrafast dynamics of soft materials have been hampered by blurry diffraction patterns. Here, we report time-resolved IR vibrational spectroscopy and electron diffractometry to acquire ultrafast snapshots of a columnar LC material bearing a photoactive core moiety. Differential-detection analyses of the combination of time-resolved IR vibrational spectroscopy and electron diffraction are powerful tools for characterizing structures and photoinduced dynamics of soft materials.

Here, we present the protocols of differential-detection analyses of time-resolved infrared vibrational spectroscopy and electron diffraction which enable observations of the deformations of local structures around photoexcited molecules in a columnar liquid crystal, giving an atomic perspective on the relationship between the structure and the dynamics of this photoactive material.

We discuss in this article the experimental measurements of the molecules in liquid crystal (LC) phase using the time-resolved infrared (IR) vibrational ...

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Rational design of disordered molecular aggregates and solids for optoelectronic applications relies on our ability to predict the properties of such materials using theoretical and computational methods. However, large molecular systems where disorder is too significant to be considered in the perturbative limit cannot be described using either first principles quantum chemistry or band theory. Multiscale modeling is a promising approach to understanding and optimizing the optoelectronic properties of such systems. It uses first-principles quantum chemical methods to calculate the properties of individual molecules, then constructs model Hamiltonians of molecular aggregates or bulk materials based on these calculations. In this paper, we present a protocol for constructing a tight-binding Hamiltonian that represents the excited states of a molecular material in the basis of Frenckel excitons: electron-hole pairs that are localized on individual molecules that make up the material. The Hamiltonian parametrization proposed here accounts for excitonic couplings between molecules, as well as for electrostatic polarization of the electron density on a molecule by the charge distribution on surrounding molecules. Such model Hamiltonians can be used to calculate optical absorption spectra and other optoelectronic properties of molecular aggregates and solids.

Here, we present a protocol for parametrizing a tight-binding excitonic Hamiltonian for calculating optical absorption spectra and optoelectronic properties of molecular materials from first-principles quantum chemical calculations.

Rational design of disordered molecular aggregates and solids for optoelectronic applications relies on our ability to predict the properties of such ...

Hyperspectral Imaging as a Tool to Study Optical Anisotropy in Lanthanide-Based Molecular Single Crystals

In this work, we describe a protocol for a novel application of hyperspectral imaging (HSI) in the analysis of luminescent lanthanide (Ln3+)-based molecular single crystals. As representative example, we chose a single crystal of the heterodinuclear Ln-based complex [TbEu(bpm)(tfaa)6] (bpm=2,2&#8217;-bipyrimidine, tfaa&#8211; =1,1,1-trifluoroacetylacetonate) exhibiting bright visible emission under UV excitation. HSI is an emerging technique that combines 2-dimensional spatial imaging of a luminescent structure with spectral information from each pixel of the obtained image. Specifically, HSI on single crystals of the [Tb-Eu] complex provided local spectral information unveiling variation of the luminescence intensity at different points along the studied crystals. These changes were attributed to the optical anisotropy present in the crystal, which results from the different molecular packing of Ln3+ ions in each one of the directions of the crystal structure. The HSI herein described is an example of the suitability of such technique for spectro-spatial investigations of molecular materials. Yet, importantly, this protocol can be easily extended for other types of luminescent materials (such as micron-sized molecular crystals, inorganic microparticles, nanoparticles in biological tissues, or labelled cells, among others), opening many possibilities for deeper investigation of structure-property relationships. Ultimately, such investigations will provide knowledge to be leveraged into the engineering of advanced materials for a wide range of applications from bioimaging to technological applications, such as waveguides or optoelectronic devices.

Here, we present a protocol to obtain luminescent hyperspectral imaging data and to analyze optical anisotropy features of lanthanide-based single crystals using a Hyperspectral Imaging System.

In this work, we describe a protocol for a novel application of hyperspectral imaging (HSI) in the analysis of luminescent lanthanide (Ln3+)-based ...

ARL Spectral Fitting as an Application to Augment Spectral Data via Franck-Condon Lineshape Analysis and Color Analysis

The ARL Spectral Fitting application provides a free, publicly accessible, and fully transparent method for performing Franck-Condon Lineshape Analysis (FCLSA) on spectral data, in addition to CIE color coordinate determination and basic spectral processing. While some of the features may be found in commercial software or in programs made by&#160;academic research groups, we believe that ARL Spectral Fitting is the only application that possesses all three of the aforementioned attributes.
This program is intended as a standalone, GUI-based application for use by an average laboratory researcher without requiring any coding knowledge or proprietary software. In addition to the standalone executable hosted on ARL GitHub, the associated MATLAB files are available for use and further development.
FCLSA augments the information found in luminescence spectra, providing meaningful insight into the relationship between the ground and excited states of a photoluminescent species. This insight is achieved by modeling spectra with two versions (modes) of an equation that are characterized by either four or six parameters, depending on which mode is used. Once optimized, the value of each of these parameters can be used to gain insight into the molecule, as well as to perform further analysis (for example, the free energy content of the excited-state molecule). This application provides tools for easy by-hand fitting of imported data, as well as two methods for optimizing this fit-damped least-squares fitting, powered by the Levenberg-Marquardt algorithm, and derivative-free fitting utilizing the Nelder-Mead simplex algorithm. Furthermore, estimations of sample color can be performed and reported in CIE and RGB coordinates.

This protocol introduces Franck-Condon Lineshape Analyses (FCLSA) of emission spectra and serves as a tutorial for the use of ARL Spectral Fitting software. The open-source software provides an easy and intuitive way to perform advanced analysis of emission spectra including excited state energy calculations, CIE color coordinate determination, and FCLSA.

The ARL Spectral Fitting application provides a free, publicly accessible, and fully transparent method for performing Franck-Condon Lineshape Analysis ...

A Technical Guide for Performing Spectroscopic Measurements on Metal-Organic Frameworks

Metal-organic frameworks (MOFs) offer a unique platform to understand light-driven processes in solid-state materials, given their high structural tunability. However, the progression of MOF-based photochemistry has been hindered by the difficulty in spectrally characterizing these materials. Given that MOFs are typically larger than 100 nm in size, they are prone to excessive light scatter, thereby rendering data from valuable analytical tools like transient absorption and emission spectroscopy nearly uninterpretable. To gain meaningful insights of MOF-based photo-chemical and physical processes, special consideration must be taken toward properly preparing MOFs for spectroscopic measurements, as well as the experimental setups that garner higher quality data. With these considerations in mind, the present guide provides a general approach and set of guidelines for the spectroscopic investigation of MOFs. The guide addresses the following key topics: (1) sample preparation methods, (2) spectroscopic techniques/measurements with MOFs, (3) experimental setups, (3) control experiments, and (4) post-run stability characterization. With appropriate sample preparation and experimental approaches, pioneering advancements toward the fundamental understanding of light-MOF interactions are significantly more attainable.

Here, we use a polymer stabilizer to prepare metal-organic framework (MOF) suspensions that exhibit markedly decreased scatter in their ground-state and transient absorption spectra. With these MOF suspensions, the protocol provides various guidelines to characterize the MOFs spectroscopically to yield interpretable data.

Metal-organic frameworks (MOFs) offer a unique platform to understand light-driven processes in solid-state materials, given their high structural ...

Decoding Transient Absorption - Processing, Fitting, and Interpreting Data

An Introduction to Processing, Fitting, and Interpreting Transient Absorption Data

Transient absorption (TA) spectroscopy is a powerful time-resolved spectroscopic method used to track the evolution of excited-state processes through changes in the system&#39;s absorption spectrum. Early implementations of TA were confined to specialized laboratories, but the evolution of commercial turn-key systems has made the technique increasingly available to research groups across the world. Modern TA systems are capable of producing large datasets with high energetic and temporal resolution that are rich in photophysical information. However, processing, fitting, and interpreting TA spectra can be challenging due to the large number of excited-state features and instrumental artifacts. Many factors must be carefully considered when collecting, processing, and fitting TA data in order to reduce uncertainty over which model or set of fitting parameters best describes the data. The goal of data preparation and fitting is to reduce as many of these extraneous factors while preserving the data for analysis. In this method, beginners are provided with a protocol for processing and preparing TA data as well as a brief introduction to selected fitting procedures and models, specifically single wavelength fitting and global lifetime analysis. Commentary on a number of commonly encountered data preparation challenges and methods of addressing them is provided, followed by a discussion of the challenges and limitations of these simple fitting methods.

Author Spotlight: Exploring Light-Driven Chemical Reactions and Energy-Harnessing Devices in Photochemical Research

This protocol is a beginner's entryway into processing, fitting, and interpreting transient absorption spectra. The focus of this protocol is the preparation of datasets, and fitting using both single wavelength kinetics and global lifetime analysis. Challenges associated with transient absorption data and its fitting are discussed.

Transient absorption (TA) spectroscopy is a powerful time-resolved spectroscopic method used to track the evolution of excited-state processes through ...

Synthesis of Quinoline-Based Ionic Liquids for Antimicrobial Applications

Green Synthesis of Quinoline-Based Ionic Liquid

The ever-growing menace of Antimicrobial Resistance (AMR) jeopardizes the potency of the prevailing antibiotics against the relentlessly sprouting infections spawned by bacteria, viruses, parasites as well as fungi, posing a great threat to human health and well-being. In this regard, several novel molecules have proved their mettle, with Ionic Liquids (ILs) being one of the most eco-friendly, non-volatile, and thermally stable alternatives to the existing antimicrobials, possessing high solvating potential as well as low vapor pressure. Moreover, the utilization of these entities in both stabilizing as well as destabilizing protein structures and enhancing enzymatic activity has further raised their potential in the biomedical industry. With this in view, we present the green synthesis and characterization of quinoline-based IL, owing to its immense antimicrobial potency, with low cytotoxicity and great artificial chaperone activity. Here, maneuvering the one-pot synthesis approach in solvent-free, greener reaction conditions not only ameliorated the reaction efficiency but also augmented the chemical yield. The purity of the synthesized IL was corroborated using 1H Nuclear Magnetic Resonance (NMR), 13C NMR, and Infrared (IR) spectroscopy. The biological potential of the synthesized compound is further validated by analyzing its Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties and authenticated using disc diffusion assay.

Author Spotlight: Advancing Antimicrobial Resistance Research with Innovative Approaches and Synthetic Compounds

In the present work, we elucidate the green synthesis of quinoline-based Ionic Liquid (IL), namely, 1-Hexadecylquinolin-1-ium bromide {[C16quin]Br} by mixing quinoline with an excess of 1-Bromohexadecane, along with its detailed characterization using Nuclear Magnetic Resonance and Infrared spectroscopic measurements.

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

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