Polarization Dependent Time-Resolved Infrared Spectroscopy and Its Applications

Polarization dependent time-resolved infrared (TRIR) spectroscopy has proven to be a useful technique to study the structural dynamics in a photochemical process. The angular information of transient species is obtainable in this measurement, which makes it a valuable technique for the investigation of electron distribution, molecular structure, and conformational dynamics. In this review, we briefly introduce the principles and applications of polarization dependent TRIR spectroscopy. We mainly focused on the following topics: (i) an overview of TRIR spectroscopy, (ii) principles of TRIR spectroscopy and its advantages compared to the other ultrafast techniques, (iii) examples that use polarization dependent TRIR spectroscopy to probe a variety of chemical and dynamical phenomena including protein conformational dynamics, excited state electron localization, and photoisomerization, (iv) the limitations and prospects of TRIR spectroscopy.     

Nanosecond time-resolved infrared studies of visnagin and khellin triplets and radical ions

Time-resolved infrared spectroscopy (TRIR) and density functional theory (DFT) calculations were used to directly observe and assign the vibrational spectra of the triplet states of visnagin and khellin, and to investigate their electron-transfer chemistry. The TRIR spectra of triplet visnagin and triplet khellin, and of their radical cations and anions, were obtained upon 266 nm laser flash photolysis in acetonitrile and in deuterated acetonitrile. The radical cations were observed in the presence of chloranil, and the radical anions were formed in the presence of NaI and KSCN. The TRIR spectra are in good agreement with the calculated vibrational spectra. We did not observe the related neutral radicals by TRIR spectroscopy upon laser flash photolysis (LFP) of khellin in the presence of hydroquinone, but we found evidence for the formation of semiquinone and neutral visnagin radicals upon LFP of visnagin and hydroquinone.     

The mechanism of photoinduced acylation of amines by N-acyl-5,7-dinitroindoline as determined by time-resolved infrared spectroscopy

[reaction: see text] The photochemistry of N-acyl-5,7-dinitroindoline (1) was studied in acetonitrile using nanosecond time-resolved infrared (TRIR) spectroscopy. Upon photolysis, two nearly but not completely overlapping sets of transient IR bands are observed that are assigned to two non-interconvertible conformers of mixed acetic nitronic anhydride 7. While syn-7 reverts rapidly to 1, anti-7 is long-lived and is able to acylate amines. Results of density functional theory calculations support conclusions based on experimental TRIR data.     

Ultrafast vibrational spectroscopy of the flavin chromophore

Ultrafast time-resolved infrared (TRIR) spectra of flavin adenine dinucleotide (FAD) and the anion of lumiflavin (Lf-) are described. Ground-state recovery and excited-state decay of FAD reveal a common dominant ultrafast relaxation and a minor slower component. The Lf- transient lacks a fast component. No intermediate species are observed, suggesting that the quenching mechanism is internal conversion promoted by interaction of the adenine and isoalloxazine rings in FAD. Modes are assigned, and the potential for extension of the TRIR method to photoactive proteins is discussed.     

Charge photoinjection in intercalated and covalently bound [Re(CO)3(dppz)(py)]+-DNA constructs monitored by time-resolved visible and infrared spectroscopy

The complex [Re(CO)(3)(dppz)(py'-OR)](+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; py'-OR = 4-functionalized pyridine) offers IR sensitivity and can oxidize DNA directly from the excited state, making it a promising probe for the study of DNA-mediated charge transport (CT). The behavior of several covalent and noncovalent Re-DNA constructs was monitored by time-resolved IR (TRIR) and UV/visible spectroscopies, as well as biochemical methods, confirming the long-range oxidation of DNA by the excited complex. Optical excitation of the complex leads to population of MLCT and at least two distinct intraligand states. Experimental observations that are consistent with charge injection from these excited states include similarity between long-time TRIR spectra and the reduced state spectrum observed by spectroelectrochemistry, the appearance of a guanine radical signal in TRIR spectra, and the eventual formation of permanent guanine oxidation products. The majority of reactivity occurs on the ultrafast time scale, although processes dependent on slower conformational motions of DNA, such as the accumulation of oxidative damage at guanine, are also observed. The ability to measure events on such disparate time scales, its superior selectivity in comparison to other spectroscopic techniques, and the ability to simultaneously monitor carbonyl ligand and DNA IR absorption bands make TRIR a valuable tool for the study of CT in DNA.     

Photochemistry of N-acetyl-, N-trifluoroacetyl-, N- mesyl-, and N-tosyldibenzothiophene sulfilimines

Time-resolved infrared (TRIR) spectroscopy, product studies, and computational methods were applied to the photolysis of sulfilimines derived from dibenzothiophene that were expected to release acetylnitrene, trifluoroacetylnitrene, mesylnitrene, and tosylnitrene. All three methods provided results for acetylnitrene consistent with literature precedent and analogous experiments with the benzoylnitrene precursor, i.e., that the ground-state multiplicity is singlet. In contrast, product studies clearly indicate triplet reactivity for trifluoroacetylnitrene, though TRIR experiments were more ambiguous. Product studies suggest that these sulfilimines are superior sources for sulfonylnitrenes, which have triplet grounds states, to the corresponding azides, and computational studies shed light on the electronic structure of the nitrenes.     

Ultrafast infrared spectral fingerprints of vitamin B12 and related cobalamins

Vitamin B(12) (cyanocobalamin, CNCbl) and its derivatives are structurally complex and functionally diverse biomolecules. The excited state and radical pair reaction dynamics that follow their photoexcitation have been previously studied in detail using UV-visible techniques. Similar time-resolved infrared (TRIR) data are limited, however. Herein we present TRIR difference spectra in the 1300-1700 cm(-1) region between 2 ps and 2 ns for adenosylcobalamin (AdoCbl), methylcobalamin (MeCbl), CNCbl, and hydroxocobalamin (OHCbl). The spectral profiles of all four cobalamins are complex, with broad similarities that suggest the vibrational excited states are related, but with a number of identifiable variations. The majority of the signals from AdoCbl and MeCbl decay with kinetics similar to those reported in the literature from UV-visible studies. However, there are regions of rapid (<10 ps) vibrational relaxation (peak shifts to higher frequencies from 1551, 1442, and 1337 cm(-1)) that are more pronounced in AdoCbl than in MeCbl. The AdoCbl data also exhibit more substantial changes in the amide I region and a number of more gradual peak shifts elsewhere (e.g., from 1549 to 1563 cm(-1)), which are not apparent in the MeCbl data. We attribute these differences to interactions between the bulky adenosyl and the corrin ring after photoexcitation and during radical pair recombination, respectively. Although spectrally similar to the initial excited state, the long-lived metal-to-ligand charge transfer state of MeCbl is clearly resolved in the kinetic analysis. The excited states of CNCbl and OHCbl relax to the ground state within 40 ps with few significant peak shifts, suggesting little or no homolysis of the bond between the Co and the upper axial ligand. Difference spectra from density functional theory calculations (where spectra from simplified cobalamins with an upper axial methyl were subtracted from those without) show qualitative agreement with the experimental data. They imply the excited state intermediates in the TRIR difference spectra resemble the dissociated states vibrationally (the cobalamin with the upper axial ligand missing) relative to the ground state with a methyl in this position. They also indicate that most of the TRIR signals arise from vibrations involving some degree of motion in the corrin ring. Such coupling of motions throughout the ring makes specific peak assignments neither trivial nor always meaningful, suggesting our data should be regarded as IR spectral fingerprints.     

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.     

Ultrafast electronic and vibrational dynamics of stabilized A state mutants of the green fluorescent protein (GFP): Snipping the proton wire

Two blue absorbing and emitting mutants (S65G/T203V/E222Q and S65T at pH 5.5) of the green fluorescent protein (GFP) have been investigated through ultrafast time resolved infra-red (TRIR) and fluorescence spectroscopy. In these mutants, in which the excited state proton transfer reaction observed in wild-type GFP has been blocked, the photophysics are dominated by the neutral A state. It was found that the A* excited state lifetime is short, indicating that it is relatively less stabilised in the protein matrix than the anionic form. However, the lifetime of the A state can be increased through modifications to the protein structure. The TRIR spectra show that a large shifts in protein vibrational modes on excitation of the A state occurs in both these GFP mutants. This is ascribed to a change in H-bonding interactions between the protein matrix and the excited state.     

Ground- and excited-state infrared spectra of an azacrown-substituted [(bpy)Re(CO)3L]+ complex: structure and bonding in ground and excited states and effects of Ba2+ binding

Ground- and excited-state infrared spectra are reported for a [(bpy)ReI(CO)3L]+ complex (bpy = 2,2'-bipyridine) in which L contains an azacrown ether that is linked to Re via an amidopyridyl group. Ground-state band assignments are made with the aid of spectra from model complexes in which a similar electron-donating dimethylamino group replaces the azacrown, in which an electron-donor group is absent, and from the L ligands, in conjunction with DFT calculations. Picosecond time-resolved IR (TRIR) spectra in the nu(CO) region show bands characteristic of a metal-to-ligand charge-transfer (MLCT) excited state, [(bpy*-)ReII(CO)3L]+, from the complex in which an electron-donor group is absent, whereas those from the azacrown complex show bands of an MLCT state evolving into those characteristic of a ligand-to-ligand charge-transfer (LLCT) excited state, [(bpy*-)ReI(CO)3(L*+)]+, formed upon intramolecular electron transfer. Picosecond TRIR spectra of the azacrown complex in the fingerprint region show strong L ligand bands that indicate that significant charge redistribution occurs within this ligand in the MLCT state and that decay as the LLCT state forms. Picosecond TRIR spectra obtained when Ba2+ was complexed to the azacrown show bands of only an MLCT state at all times up to 2 ns, consistent with the presence of Ba2+ inhibiting electron transfer from the azacrown N atom to form the LLCT state, and the positions of the bands in the fingerprint region provide direct evidence for the proposal that charge redistribution within the L ligand induces Ba2+ release from the azacrown in the MLCT state.     

Time-domain calculations of the polarized Raman spectra, the transient infrared absorption anisotropy, and the extent of delocalization of the OH stretching mode of liquid water

The polarized Raman spectrum and the time dependence of the transient infrared (TRIR) absorption anisotropy are calculated for the OH stretching mode of liquid water (neat liquid H2O) by using time-domain formulations, which include the effects of both the diagonal frequency modulations (of individual oscillators) induced by the interactions between the dipole derivatives and the intermolecular electric field, and the off-diagonal (intermolecular) vibrational coupling described by the transition dipole coupling (TDC) mechanism. The IR spectrum of neat liquid H2O and the TRIR anisotropy of a liquid mixture of H2O/HDO/D2O are also calculated. It is shown that the calculated features of these optical signals, including the temperature dependence of the polarized Raman and IR spectra, are in reasonable agreement with the experimental results, indicating that the frequency separation between the isotropic and anisotropic components of the polarized Raman spectrum and the rapid decay (approximately 0.1 ps) of the TRIR anisotropy of the OH stretching mode of neat liquid H2O are mainly controlled by the resonant intermolecular vibrational coupling described by the TDC mechanism. Comparing with the time evolution of vibrational excitations, it is suggested that the TRIR anisotropy decays in the time needed for the initially localized vibrational excitations to delocalize over a few oscillators. It is also shown that the enhancement of the dipole derivatives by the interactions with surrounding molecules is an important factor in generating the spectral profiles of the OH stretching Raman band. The time-domain behavior of the molecular motions that affect the spectroscopic features is discussed.     

Solvent dependence of the 2-naphthyl(carbomethoxy)carbene singlet-triplet energy gap

The solvent dependence of the 2-naphthyl(carbomethoxy)carbene (2) singlet-triplet energy gap has been examined by time-resolved infrared (TRIR) and computational methods. The ground state of 2 changes from the triplet state in hexane to the singlet state in acetonitrile. Preferential stabilization of the singlet carbene is the result of its increased dipole moment in polar solvents. Variable-temperature TRIR experiments provide measurements of the enthalpic and entropic differences between (1)2 and (3)2 and suggest that solvent and geometry effects on the entropy of singlet and triplet carbenes can offset differences arising from spin multiplicity. B3LYP calculations using the polarizable continuum solvation model (PCM) reproduce the general trends in enthalpic differences seen experimentally.     

Computational and experimental studies of the effect of substituents on the singlet-triplet energy gap in phenyl(carbomethoxy)carbene

The effect of aromatic substitution on the singlet-triplet energy gap in substituted phenyl(carbomethoxy)carbene (X-Ph-C-CO(2)CH(3), PCC) has been explored by time-resolved infrared (TRIR) spectroscopy and gas-phase computational methods. The ground state of para-substituted PCC is calculated to change from the triplet state in p-NO(2)-PCC (Delta G(ST) = 6.1 kcal/mol) to the singlet state in p-NH(2)-PCC (Delta G(ST) = -2.8 kcal/mol). The absence of solvent perturbation in the TRIR spectra of p-N(CH(3))(2)-PCC (which should have electronic properties similar to p-NH(2)-PCC) and parent PCC is consistent with their ground states lying > +/-2 kcal/mol from the next available electronic state, in line with the computational results. The observation of solvent perturbation in the TRIR spectra of p-OCH(3)-PCC and p-CH(3)-PCC implies that their ground states lie < +/-1 kcal/mol from their next available electronic state. This is in agreement with our computational results, which predict a gas-phase Delta G(ST) of -0.8 and 1.6 kcal/mol for p-OCH(3)-PCC and p-CH(3)-PCC as compared to Delta G(ST) values of -3.9 and -1.3 kcal/mol from polarizable continuum model (PCM) calculations with acetonitrile as a solvent. Gas-phase computational results for the meta- and ortho-substituted PCC species are also presented, along with selected linear free energy (LFE) relationships for the para and meta species.     

Time-resolved optical and infrared spectral studies of intermediates generated by photolysis of trans-RhCl(CO)(PR3)2. Roles Played in the Photocatalytic Activation of Hydrocarbons

Described are picosecond and nanosecond time-resolved optical (TRO) spectral and nanosecond time-resolved infrared (TRIR) spectral studies of intermediates generated when the rhodium(I) complexes trans-RhCl(CO)L2 (L = PPh3 (I), P(p-tolyl)3 (II), or PMe3 (III)) are subjected to photoexcitation. Each of these species, which are precursors in the photocatalytic activation of hydrocarbons, undergoes CO labilization to form an intermediate concluded to be the solvated complex RhCl(Sol)L2 (A(i)). The picosecond studies demonstrate that an initial transient is formed promptly (<30 ps), which decays to A(i) with lifetimes ranging from 40 to 560 ps depending upon L and the medium. This is proposed on the basis of ab initio calculations to be a metal-to-ligand charge transfer (MLCT) excited state. Second-order rate constants (kCO) for reaction of the A(i) with CO were determined, and these depend on the nature of L and the solvent, the slowest rate being for A(I) in tetrahydrofuran (kCO = 7.1 x 10(6) M(-1) x s(-1)), the fastest being for A(III) in dichloromethane (1.3 x 10(9) M(-1) x s(-1)). Each A(i) also undergoes competitive unimolecular reaction with solvent to form long-lived transients with TRIR properties suggesting these to be Rh(III) products of oxidative addition. Although this was mostly suppressed by the presence of higher concentrations of CO (which trapped A(i) to re-form the starting complexes in each case), both TRO and TRIR experiments indicate that a fraction of the oxidative addition could not be quenched. Thus, the short-lived MLCT state or a vibrationally hot species formed during the decay of this excited state appears to participate directly in C-H activation.     

Caught in the Loop: Binding of the [Ru(phen)2(dppz)]2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy

Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)₂(dppz)]²⁺ “light-switch” complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K⁺ and Na⁺ containing solutions. TRIR permits the simultaneous monitoring both of the “dark” and “bright” states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na⁺ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.     

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

Vibrational spectra of the lowest energy triplet states of thymine and its 2′-deoxyribonucleoside, thymidine, are reported for the first time. Time-resolved infrared (TRIR) difference spectra were recorded over seven decades of time from 300 fs to 3 μs using femtosecond and nanosecond pump-probe techniques. The carbonyl stretch bands in the triplet state are seen at 1603 and 1700 cm⁻¹ in room-temperature acetonitrile-d₃ solution. These bands and additional ones observed between 1300 and 1450 cm⁻¹ are quenched by dissolved oxygen on a nanosecond time scale. Density-functional calculations accurately predict the difference spectrum between triplet and singlet IR absorption cross sections, confirming the peak assignments and elucidating the nature of the vibrational modes. In the triplet state, the C4O carbonyl exhibits substantial single-bond character, explaining the large (70 cm⁻¹) red shift in this vibration, relative to the singlet ground state. Femtosecond TRIR measurements unambiguously demonstrate that the triplet state is fully formed within the first 10 ps after excitation, ruling out a relaxed ¹nπ^* state as the triplet precursor.     

Influence of a gold(I)-Acetylide subunit on the photophysics of Re(phen)(CO)3Cl

The synthesis and photophysical properties of two new Re(I) complexes are reported: fac-Re(phenC triple-bond CH)(CO)(3)Cl (where phenC triple bond CH is 5-ethynyl-1,10-phenanthroline) and its Au(I)-acetylide analogue (fac-Re(phenC triple-bond CAuPPh(3))(CO)(3)Cl). Also reported are the photophysical measurements obtained for the benchmark fac-Re(phen)(CO)(3)Cl chromophore, as well as the phenC triple-bond CAuPPh(3) and phenC triple-bond CH ligands. The unstable nature of the precursor gold-containing ligand illustrates the advantage of using the "chemistry on the complex" approach, which facilitated preparation of the Re-Au binuclear complex. Where possible, all compounds were studied by static and transient absorption (TA), as well as steady-state and time-resolved photoluminescence (TRPL), at room temperature (RT) and 77 K, as well as nanosecond time-resolved infrared (TRIR) spectroscopy. The spectroscopic information provided by these techniques enabled a thorough evaluation of excited-state decay in most cases. In fac-Re(phenC triple bond CH)(CO)(3)Cl, the RT excited-state decay is most consistent with a metal-to-ligand charge transfer (MLCT) assignment, whereas at 77 K, the lowest excited state is dominated by the triplet intraligand ((3)IL) state, localized within the diimine ligand. The lowest excited state in fac-Re(phenC triple-bond CAuPPh(3))(CO)(3)Cl seems to result from an admixture of Re-based MLCT and (3)IL states resident on the phenC triple-bond CAuPPh(3) moiety. TA and TRIR methods indicate that these excited states are thermally equilibrated at room temperature. At 77 K, the MLCT energy of fac-Re(phenC triple-bond CAuPPh(3))(CO)(3)Cl is increased as a result of the glassy medium and the resulting excited state can be considered to be ligand-localized.     

A probe method for studying dibromocarbene by time resolved infrared spectroscopy

Dibromocarbene reacts with tertiary-butylisocyanide to form a ketenimine. The absolute rate constant of the reaction (k_TBI = 2.3 × 10⁹ M⁻¹ s⁻¹) was determined by laser flash photolysis techniques with UV-vis detection of the dibromocarbene-pyridine ylide. The ketenimine was detected by TRIR spectroscopy at 2040 cm⁻¹. Isocyanide trapping of carbenes to form ketenimines is proposed as a general method of studying IR silent carbenes by TRIR spectroscopy.     

Reversal of a Single Base‐Pair Step Controls Guanine Photo‐Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)₂(dppz)]²⁺ have been compared in 5′‐{CCGG AT CCGG}₂ and 5′‐{CCGG TA CCGG}₂ using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.     

A search for carbene-solvent interactions using time-resolved infrared spectroscopy

[reaction: see text] The time-resolved infrared (TRIR) spectra of chlorophenylcarbene (CPC) and fluorophenylcarbene (FPC) were recorded in heptane at ambient temperature. The C[bond]C and C[bond]F vibrational frequencies involving the carbene carbon were obtained in heptane, benzene, and acetonitrile and in heptane containing 0.1M tetrahydrofuran or benzene. It is concluded that carbene-solvent interactions of CPC and FPC are quite weak.