Computational Chemistry Using Spartan 06 Biology Essay

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Figure 1 - SC114, Compound 1 - the molecular dyad in which the donor and acceptor units are directly coupled, showing clearly the orthogonal orientation and the distance between the redox partnersElectrostatic effects have been calculated on the basis of point dipoles with the charge (after light-induced electron transfer) being localised in the centre of each unit - the conventional approach. This project has also considered an alternative approach in which the electrostatic potential can be computed from partial electronic charges. The project has made use of modern computational chemistry to calculate partial charges resident on the donor and acceptor units of the molecular dyad. Models of the two compounds were developed in Spartan '06, and the full electrostatic potential in terms of the interactions between each partial dipole, spread around the molecule, and allowing for both distance and angle. This more sophisticated model was compared with the conventional approach in anticipation that there is improved agreement between experiment and theory. SPARTAN is a molecular modelling and computational chemistry application which allows for quantitative calculations, leading directly to information about the geometries of transition states, and about reaction mechanisms in general. Quantum chemical calculations can supply information to complement existing experimental data or replace it altogether, hence allowing us to investigate if there is an improved agreement between experiment and theory. Spartan is a modern molecular modelling program designed to apply computational chemistry methods (theoretical models) to a number of a standard tasks that provide chemists with calculated data applicable to the determination of molecular shape (conformation), structure (equilibrium and transition state geometry), spectral properties, molecular and atomic properties, reactivity and selectivity. Structures are drawn and minimised in order for a quantitative calculation to be run - a Semi-emperical PM3 calculation run at Equilibrium Geometry at Ground state - as this is the fastest and most accurate. This allows for all distances between atoms, lengths between bonds and angles to be measured accurately, to be later used in further electrostatic potential calculations. Figure 1 is a ball and stick representation of Compound 1 - SC113. It clearly shows how the aniline donor is covalently held in an othorgonal orientation to the BODIPY acceptor unit. The distance between the donor N and the carbons of the BODIPY were noted, in order to use the following equation (2) to calculate the energy difference between the charge separation if the charge (from the donor N) lies in the centre of the acceptor unit (the average distance of the meso carbon and the boron), if it were to remain on a particular carbon or the boron alone, or if it is delocalised over all 9 carbons of the indacene core. If we are assuming the negative charge is delocalised over 9 carbons, we use 9 individual distances at approximate dielectric constants of 4, 6, 8, 10, 20 and 30 which are then added together (in eV), to be plotted against dielectric constant and compared with a graph of the ΔE calculated when assuming the negative charge takes a central position on the BODIPY.

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Graphs in Appendix 3 show the results of this.

Compound 1, the directly coupled donor and acceptor units, has a higher electrostatic potential than Compound 2 (figure 3) with a naphthalene bridge.

Very similar regardless of where charge ends up

ΔE less when increased distance in SC133

ΔE less in solvents of a higher ε, more polar - stabilises charge separation

Figure 2 - SC133, Compound 2 - the molecular dyad in which the donor and acceptor units are held in close proximity via a naphthalene spacer, showing clearly the orthogonal orientation and the distance between the redox partnersThis naphthalene spacer allows a rigid conformation due to chirality restraints, which can increase the rate of ET. According to super-exchange theory, the rate of ET decreases exponentially with increasing separation between the complementary redox partners. Simplest mechanism involves super-exchange interactions.

Electron transfer proceeds from donor to acceptor by way of "virtual" population of the orbitals on the bridge.

Absorption profiles

Figure 4 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.

Figure 3 - Absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.Throughout the investigation of these two molecular dyads, BODIPY was used as a control as its properties are known and understood. The compound used was synthesised and characterised by Graeme Copley in the MPL; the structures given in Appendix 1. Important characteristics of molecular dyads are given by first considering their absorption spectra. It is expected that electronic perturbation of the aromatic nucleus of the chromophore will result in a broadening shift. Figure 1 shows the absorption profiles of compound 1, in a range of solvents, differing in terms of their polarity, from a dielectric constant ε, of 2.02 to 24.83. The peaks are consistent with the general behaviour of BODIPY chromophores, peaking at around 525nm (with the exception of in DCM) which is attributed to the 0-0 band of a strong S0→S1 transition. It was noted that the shoulder of each main peak was generally, quite accurately and consistently around 490nm, and this was used as the excitation wavelength when recording fluorescence spectra. This shoulder seen at a lower wavelength is the 0-1 band of the same transition. The broad, weaker peak, below 400nm can therefore be assigned to as the S0→S2 transition of the BODIPY, the charge-transfer band, the associated charge separated state being stabilized to a greater extent in more polar solvents. Figure 2, of normalised absorption, shows how there can be a hypsochromic shift for the sharp BODIPY absorption band with an increase in solvent polarity, and in this case is represented by dichloromethane (DCM). An optically dilute sample (Amax ≤ 0.1) for each compound in each solvent was obtained by serial dilution for the absorption spectra to be recorded. The molar absorption coefficient could then be calculated from the Beer-Lambert law:

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(2) A = εcl

where A is the measured absorbance (Amax ≤ 0.1) at a given wavelength, ε is the molar absorption coefficient in standard units of M-1cm-1, c is the molar concentration, and l is the path length of the cell.

Steady-state fluorescence

Figure 5 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.

Figure 6 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.

Figure 7 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.On conclusion, from the absorption spectra, that we should excite at 490nm, the emission spectra were run for both compounds in the initial series of solvents; cyclohexane, dioxane, dibutyl ether, diethyl ether, chloroform, ethyl acetate, THF, DCM and a very polar butyronitrile. It was noted that we could use further solvents, needed to reduce the intensity of the fluorescence. By lowering the fluorescence, underlying peaks will be of a similar intensity, helping us to spot the charge transfer band. Spectra in which we can see this assumed charge transfer band can be found in Appendix 6 and Appendix 7. All emission spectra were normalised on a graph with absorption spectra which displays their small Stokes' shift. This is typical of similar monomeric BODIPY dyes. Figure 6 shows the emission spectra of compound 1 in ether (ε = 4.34), which drops quite steeply after the shoulder of the intense peak, however Figure 7 indicates there is additional shoulder, reflecting an underlying broad peak (not present in ether) characteristic of a charge transfer band - electron transfer has taken place. This charge-separated state is visible in some solvents, and in some of these more than others. All spectra, of each compond in the series of solvents, were critically analysed and it was decided in which solvents we could best see this broad peak - implying a charge-separated state had been achieved. Two further solvents were used - 2 methyl THF and carbon tertrachloride in which this was hoped to be seen more clearly. To ensure that the broad profile was the result of genuine fluorescence from single molecule, rather than the product of an intermolecular interaction, the effect of soute concentration was evaluated. For three successively more dilute solutions of each compound in each solvent, spectra were obtained and deconvoluted into the minimum number or Gaussian shaped bands required to gain good representation of the spectrum. Within experimental error, the half-width for the fitted Gaussian bands remains constant regardless of solute concentration. The excitation spectrum of each dimer reproduces its respective absorption spectrum. Together, this information provides conclusive evidence that the emission is genuine, not the result of aggregated forms of the compound, and originates from an excited state, which is occupied regardless of the excitation wavelength.

The fluorescence of BODIPY alone was recorded and this can be seen, compared with the fluorescence of the compounds in different solvents, in Appendix 7. All graphs indicate fluroescence quenching is generally occuring, as the dyad fluorescence intensity is lower than the intensity of BODIPY alone (used as a control). This suggests electron transfer is taking place - Electron transfer is a known quencher of fluorescence. In compound 1 (SC114), as the dielectric constant of the solvent increases, the fluorescence intensity of the pure compound decreases vastly in comparison to the BODIPY control - showing how heavily dependent electron transfer is on solvent polarity. However, in the compound with the spacer - fluorescence intensity is greater for the dyad in the first two solvents than the BODIPY, but follows the same trend for the rest.

Reorganisation energy from Stokes' shift

Figure 8 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.

Figure 9 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.When electron or charge transfer is accompanied by a change in molecular geometry, the solvent in which the reaction is carried out can have a profound effect upon the thermodynamics of the system. This is a direct consequence of the reorganisation energy associated with the solvent realignment inherent from a change in electron density distribution within a system. The reorganisation energy is affected by both solvent polarity, and by the degree to which frictional forces between the chromophore and solvent molecular are perturbed. It is therefore conceivable that, by paying close attention to these parameters, the pathways and rates of electron-transfer reactions can be manipulated by means of careful solvent selection and many such studies have been reported. From recording the fluorescence of the dyad, and plotting the areas in each different solvent on the same graph, we can see a trend - electron transfer occurs more in polar solvents - as the amount of fluorescence is lower - it has been quenched by electron transfer. These systems have a high dependence on solvent polarity. However, above a dielectric constant of around 10 there is too much uncertainty - the charge-transfer peak is too broad due to the associated charge-separated state being stabilised to a greater extent in more polar solvents, in which there is a permanent separation of positive and negative charge. Solvents are generally grouped as either polar or non-polar; the extent of which usually being described by a dielectric constant. The general trend is shown here in Figure 8, 9 and 10; the solvent polarity being represented in 3 ways - as a dielectric constant, a value known as an SdP, or as a function of the Pekar equation given below. The dielectric constant is the extent to which a solvent polarises; by definition it is the ability of a solvent to stabilise a charged particle, reducing the strength caused by an electric field. In order to determine a relative value, the individual is compared to the field strength of a charged particle in vacuum. The dielectric constant is not the only measure of polarity. More 'specific' terms and values have been described, more accurate to the chemist. A new, generalised treatment of the solvent effect was proposed by Catalán (REF) for the use in the analysis of the solvatochromic shifts of UV-vis absorption and fluorescence emission maxima. Solvent dipolarity and polarisability are the important causes of solvatochromism. This measurement was tested in Figure 9 and the result was a very similar trend to the dielectric constant proving it can be used accordingly.

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Next, the solvent polarity was represented as a function of the Pekar equation given below; using the refractive index n, and based on the given dielectric constant. For this reason this trend is more like figure 8, again following our predicted trend, describing the effect of the non-equilibrium solvent polarisation.

Figure 10 - Normalised absorption spectra recorded for compound 1 (SC114) in a range of solvents, under controlled reduction at room temperature.

Pekar equation f,

(1)

Fluorescence properties

Appendix 7 - fluorescence intensity of pure SC114 in the selected solvent compared with BODIPY alone

As the dielectric constant of the solvent increases, the fluorescence intensity of the pure compound decreases vastly - showing how heavily dependent electron transfer is on solvent polarity.

3 - dibutyl ether ε = 3.1

4 - diethyl ether ε = 4.34

11 - 2-methyl THF ε = 6.97

7 - THF ε = 7.52

P - butyronitrile ε = 24.83

However, in the compound with the spacer - fluorescence intensity is greater for the dyad in the first two solvents than the BODIPY, but follows the same trend for the rest.

Appendix 7 - fluorescence intensity of pure SC133 in the selected solvent compared with BODIPY alone

Data analysis

Excimers (excited-state dimers) and other small aggregates have also been reported to exhibit broad, bell-shaped bands in the absorption spectra. A constant peak intensity ratio implies that the broad band seen in each solvent is not the result of an aggregate, and is most likely due to a direct photo-induced transition to a charge-transfer state. This can be seen more clearly when spectra are fitted using PeakFit v4, a program which enables deconvolution of absorption or emission spectra into a series of Gaussian-shaped bands. These 'bell-shaped' bands correspond to the transitions between discrete vibrational levels within the molecular dyad. The software provides a direct numerical output of values for the position, intensity and full-width at half maximum (FWHM - described in Figure 11) of the bands. From these, many photophysical parameters can be obtained including the energy associated with individual electronic transitions, the energy gap between