Dissipative dynamics of a system passing through a conical intersection: ultrafast pump-probe observables

The dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment, is studied with the purpose of identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semigroup formalism and the surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reflecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.     

Broadband pump-probe spectroscopy with sub-10-fs resolution for probing ultrafast internal conversion and coherent phonons in carotenoids

We use pump-probe spectroscopy with broadband detection to study electronic energy relaxation and coherent vibrational dynamics in carotenoids. A fast optical multichannel analyzer combined with a non-collinear optical parametric amplifier allows simultaneous acquisition of the differential transmission dynamics on the 500–700 nm wavelength range with sub-10-fs temporal resolution. The broad spectral coverage enables on the one hand a detailed study of the ultrafast bright-to-dark state internal conversion process; on the other hand, the tracking of the motion of the vibrational wavepacket launched on the ground state multidimensional potential energy surface. We present results on all-trans β-carotene and on a long-chain polyene in solution. The developed experimental setup enables the straightforward acquisition and analysis of coherent vibrational dynamics, highlighting time–frequency domain features with extreme resolution.     

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.     

Single-molecule pump-probe experiments reveal variations in ultrafast energy redistribution

Single-molecule pump probe (SM2P) is a novel, fluorescence-based technique that allows the study of ultrafast processes on the single-molecule level. Exploiting SM2P we have observed large variations (from 1 ps to below 100 fs) in the energy redistribution times of chemically identical molecules in the same sample. Embedding the molecules in a different matrix or changing the excitation wavelength does not lead to significant changes in the average redistribution time. However, chemically different molecules exhibit different characteristic redistribution times. We therefore conclude that the process measured with the SM2P technique is dominated by intramolecular energy redistribution and not intermolecular transfer to the surrounding matrix. The matrix though is responsible for inducing conformational changes in the molecule, which affect the coupling between electronic and vibrational modes. These conformational changes are the main origin of the observed broad distribution of redistribution times.     

Vibrational dynamics of acetate in D2O studied by infrared pump-probe spectroscopy

Solute-solvent interactions between acetate and D(2)O were investigated by vibrational spectroscopic methods. The vibrational dynamics of the COO asymmetric stretching mode in D(2)O was observed by time-resolved infrared (IR) pump-probe spectroscopy. The pump-probe signal contained both decay and oscillatory components. The time dependence of the decay component could be explained by a double exponential function with time constants of 200 fs and 2.6 ps, which are the same for both the COO asymmetric and symmetric stretching modes. The Fourier spectrum of the oscillatory component contained a band around 80 cm(-1), which suggests that the COO asymmetric stretching mode couples to a low-frequency vibrational mode with a wavenumber of 80 cm(-1). Based on quantum chemistry calculations, we propose that a bridged complex comprising an acetate ion and one D(2)O molecule, in which the two oxygen atoms in the acetate anion form hydrogen bonds with the two deuterium atoms in D(2)O, is the most stable structure. The 80 cm(-1) low-frequency mode was assigned to the asymmetric stretching vibration of the hydrogen bond in the bridged complex.     

The dynamics of water-protein interaction studied by ultrafast optical Kerr-effect spectroscopy

Changes in the ultrafast dynamics and terahertz Raman spectrum accompanying a helix-to-coil transition of a homo-polypeptide have been observed for the first time. Formation of the alpha-helix is associated with a shift to lower frequency of a broad Raman band attributable to solvent-peptide intermolecular hydrogen bonding. This band facilitates direct spectroscopic observation of so-called hydration water near a peptide and yields the first quantitative estimate of the time scale of the ultrafast dynamics in the solvation shell, which range from 0.18 to 0.33 ps (185-100 cm(-1)) depending on the secondary structure of the peptide. Such fast motions of solvent molecules have been referred to as the "lubricant of life" and are thought to play key roles in determining structure and activity of proteins.     

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.     

Band-edge ultrafast pump-probe spectroscopy of core/shell CdSe/CdS rods: assessing electron delocalization by effective mass calculations

CdSe/CdS dot/rods nanocrystals show interesting physical properties related to the band-alignment at the hetero-interface, which controls the band-edge electron delocalization over the rods. Here the differential transmission spectra of CdSe/CdS nanorod samples with different core sizes have been measured using excitation resonant to the core transition. The photo bleaching ratio between dot and rod transitions increases with the dot size, indicating a trend towards electron localization. This trend has been further quantified by performing effective mass calculations in which the conduction band misalignment was varied in order to reproduce the observed bleaching feature ratio. The best agreement was found for negligible conduction band misalignment for small dots of around 2.3 nm in diameter, and about -0.1 eV misalignment was estimated for the larger dots, above 3.5 nm in diameter. This shows that the band misalignment might be dependent on the geometry of the system, and we argue that this might be related to different strain developed at the hetero-interface.     

On the ultrafast infrared spectroscopy of anion hydration shell hydrogen bond dynamics

Molecular Dynamics simulations are used to examine the title issue for the I-/HOD/D2O solution system in connection with recent ultrafast infrared spectroscopic experiments. It is argued that the long "modulation time" associated with the spectral diffusion of the OH frequency, extracted in these experiments, should be interpreted as reflecting the escape time of an HOD from the first hydration shell of the I- ion, i.e., the residence time of an HOD in this solvation shell. Shorter time features related to the oscillation of the OH ...I- hydrogen bond and the breaking and making of this bond are also discussed.     

Model calculation on the pump-probe measurement of ultrafast electronic population decay in polyatomic molecules

We consider the common situation of strong vibronic coupling of an optically bright (in absorption from the ground state) excited electronic state to a lower-lying dark electronic state in a polyatomic molecule. It is shown that for sufficiently short pump and probe laser pulses a time-resolved experiment measures the total time-dependent population probability P(t) of the bright state. For a realistic model problem (representing the three lowest electronic states of the benzene cation) a conical intersection of the potential energy surfaces of the bright and the dark state causes an ultrafast initial decay of P(t) on a femtosecond time scale, followed by quasiperiodic recurrences. These recurrences show up as femtosecond quantum beats in the time-resolved pump-probe signal. The beating frequency is related to the vibrational frequency of the dominant accepting mode of the system.     

Nonradiative decay dynamics of methyl-4-hydroxycinnamate and its hydrated complex revealed by picosecond pump-probe spectroscopy

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H(2)O) in the S(1) state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S(1)-S(0) origin is 8-9 ps. On the other hand, the lifetime of the OMpCA-H(2)O complex at the origin is 930 ps, which is ～100 times longer than that of OMpCA. Furthermore, in the complex the S(1) lifetime shows rapid decrease at an energy of ～200 cm(-1) above the origin and finally becomes as short as 9 ps at ～500 cm(-1). Theoretical calculations with a symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that the observed lifetime behavior of the two species is described by nonradiative decay dynamics involving trans → cis isomerization. That is both OMpCA and OMpCA-H(2)O in the S(1) state decay due to the trans → cis isomerization, and the large difference of the lifetimes between them is due to the difference of the isomerization potential energy curve. In OMpCA, the trans → cis isomerization occurs smoothly without a barrier on the S(1) surface, while in the OMpCA-H(2)O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H(2)O is in good agreement with that observed experimentally.     

Interrogating conformationally dependent electron-transfer dynamics via ultrafast visible pump/IR probe spectroscopy

We demonstrate for the first time the utility of time-resolved visible pump/mid-infrared (IR) probe spectroscopy to interrogate directly, and provide unique infomation regarding, conformationally dependent photoinduced ET dynamics and the subsequent structural evolution of the resulting charge-separated (CS) state. Exemplary polarized visible pump/IR probe experiments involving N-[5-(10,20-diphenylporphinato)zinc(II)]-N'(octyl)pyromellitic diimide (PZn-PI) and [5-[4'-(N-(N'-octyl)pyromellitic diimide)phenyl)ethynyl]-10,20-diphenylporphinato]zinc(II) (PZn()PI) show that it is possible to assess the mean PZn-to-PI interplanar torsional angle of electronically excited structural conformers that undergo ET within the sub-ps time domain for both of these donor-spacer-acceptor (D-Sp-A) systems. Further transient specroscopic experiments carried out on PZn()PI determine how this angle evolves with time. Because vibrational transition moments are often known and typically localized, this work underscores that polarized visible pump/IR probe spectroscopy defines a valuable tool to interrogate structrure in both electronically excited and CS states; this fact, coupled with the ultrafast time resolution and high senseitivity offered by this technique, make it ideally suited to probe a range of mechanistic issues relevant to charge-transfer reactions.     

Multiplex PCR with multichannel microchip electrophoresis: an ultrafast analysis for genetic diseases

A Y chromosomal polymorphic markers screening strategy using a multiplex polymerase chain reaction (PCR) and DNA microchip electrophoresis technology has recently been developed. It is a part of the human Y chromosome haplotyping system for studying Japanese population genetics and its relationship with male spermatogenic failure. This strategy is based on optimizing and modifying the primer set concentrations while keeping all other components of the PCR mixtures and conditions similar to those of a singleplex PCR. Well-balanced PCR products are obtained without changing even the DNA oligomer melting temperatures. Here, a panel of primer sets are used to amplify two groups of Y chromosome markers. The first consists of five markers and the second consists of seven markers. Both are possibly deleted in infertile men. The microchip electrophoresis technology is fast and sensitive, enables direct molecular typing of several Y chromosomal markers, and is separated by a difference of as many as six base pairs.     

Ring-closing and dehydrogenation reactions of highly excited cis-stilbene: ultrafast spectroscopy and structural dynamics

The ultrafast dynamics of highly excited cis-stilbene (CS) in a molecular beam is explored using femtosecond time-resolved mass spectrometry and structure-sensitive photoelectron spectroscopy. cis-Stilbene is initially pumped by a 6 eV photon to the 7(1)B state and the reaction is followed by ionization with a time-delayed 3 eV probe pulse. Upon excitation, cis-stilbene rapidly decays to the 3(1)B state, where it undergoes a ring-closing reaction to form 4a,4b-dihydrophenanthrene (DHP). Whereas 14% of the ionized CS molecules dissociate one hydrogen atom to form hydrophenanthrene, the ionized DHP molecules completely dehydrogenate in the ion state to produce hydrophenanthrene and phenanthrene with a 1:1 ratio. We determined the lifetimes of the 7(1)B state and the 3(1)B state of CS to be 167 and 395 fs, respectively.     

Primary reactions of bacteriophytochrome observed with ultrafast mid-infrared spectroscopy

Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C(15)═C(16) double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important recent development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Bphs covalently bind a biliverdin (BV) chromophore, naturally abundant in mammalian cells. Here, we report an ultrafast time-resolved mid-infrared spectroscopic study on the Pr state of two highly related Bphs from Rps. palustris , RpBphP2 (P2) and RpBphP3 (P3) with distinct photoconversion and fluorescence properties. We observed that the BV excited state of P2 decays in 58 ps, while the BV excited state of P3 decays in 362 ps. By combining ultrafast mid-IR spectroscopy with FTIR spectroscopy on P2 and P3 wild type and mutant proteins, we demonstrate that the hydrogen bond strength at the ring D carbonyl of the BV chromophore is significantly stronger in P3 as compared to P2. This result is consistent with the X-ray structures of Bph, which indicate one hydrogen bond from a conserved histidine to the BV ring D carbonyl for classical bacteriophytochromes such as P2, and one or two additional hydrogen bonds from a serine and a lysine side chain to the BV ring D carbonyl for P3. We conclude that the hydrogen-bond strength at BV ring D is a key determinant of excited-state lifetime and fluorescence quantum yield. Excited-state decay is followed by the formation of a primary intermediate that does not decay on the nanosecond time scale of the experiment, which shows a narrow absorption band at ～1540 cm(-1). Possible origins of this product band are discussed. This work may aid in rational structure- and mechanism-based conversion of BPh into an efficient near-IR fluorescent marker.     

Unraveling ultrafast dynamics in photoexcited aniline

A combination of ultrafast time-resolved velocity map imaging (TR-VMI) methods and complete active space self-consistent field (CASSCF) ab initio calculations are implemented to investigate the electronic excited-state dynamics in aniline (aminobenzene), with a perspective for modeling (1)πσ* mediated dynamics along the amino moiety in the purine derived DNA bases. This synergy between experiment and theory has enabled a comprehensive picture of the photochemical pathways/conical intersections (CIs), which govern the dynamics in aniline, to be established over a wide range of excitation wavelengths. TR-VMI studies following excitation to the lowest-lying (1)ππ* state (1(1)ππ*) with a broadband femtosecond laser pulse, centered at wavelengths longer than 250 nm (4.97 eV), do not generate any measurable signature for (1)πσ* driven N-H bond fission on the amino group. Between wavelengths of 250 and >240 nm (<5.17 eV), coupling from 1(1)ππ* onto the (1)πσ* state at a 1(1)ππ*/(1)πσ* CI facilitates ultrafast nonadiabatic N-H bond fission through a (1)πσ*/S(0) CI in <1 ps, a notion supported by CASSCF results. For excitation to the higher lying 2(1)ππ* state, calculations reveal a near barrierless pathway for CI coupling between the 2(1)ππ* and 1(1)ππ* states, enabling the excited-state population to evolve through a rapid sequential 2(1)ππ* → 1(1)ππ* → (1)πσ* → N-H fission mechanism, which we observe to take place in 155 ± 30 fs at 240 nm. We also postulate that an analogous cascade of CI couplings facilitates N-H bond scission along the (1)πσ* state in 170 ± 20 fs, following 200 nm (6.21 eV) excitation to the 3(1)ππ* surface. Particularly illuminating is the fact that a number of the CASSCF calculated CI geometries in aniline bear an exceptional resemblance with previously calculated CIs and potential energy profiles along the amino moiety in guanine, strongly suggesting that the results here may act as an excellent grounding for better understanding (1)πσ* driven dynamics in this ubiquitous genetic building block.     

Theory of ultrafast time-resolved absorption spectroscopy

In this paper, the density matrix formalism has been applied to treat ultrafast time-resolved absorption spectroscopy. We have shown that in the femto-second (fs) pump-probe experiments, the observed time-resolved absorption spectra consist of the contributions from the population (i.e., incoherent contribution) and the coherence (i.e., the phase of the system). The adiabatic approximation has been used to derive the expressions for ultrafast time-resolved spectra. We have also shown that the dynamics of the coherence will result in quantum beat. Numerical calculations have been performed to demonstrate the theoretical results.     

Nonadiabatic molecular dynamics simulations of correlated electrons in solution. 2. A prediction for the observation of hydrated dielectrons with pump-probe spectroscopy

The hydrated dielectron is a highly correlated, two-electron, solvent-supported state consisting of two spin-paired electrons confined to a single cavity in liquid water. Although dielectrons have been predicted to exist theoretically and have been used to explain the lack of ionic strength effect in the bimolecular reaction kinetics of hydrated electrons, they have not yet been observed directly. In this paper, we use the extensive nonadiabatic mixed quantum/classical excited-state molecular dynamics simulations from the previous paper to calculate the transient spectroscopy of hydrated dielectrons. Because our simulations use full configuration interaction (CI) to determine the ground and excited state two-electron wave functions at every instant, our nonequilibrium simulations allow us to compute the absorption, stimulated emission (SE), and bleach spectroscopic signals of both singlet and triplet dielectrons following excitation by ultraviolet light. Excited singlet dielectrons are predicted to display strong SE in the mid infrared and a transient absorption in the near-infrared. The near-infrared transient absorption of the singlet dielectron, which occurs near the peak of the (single) hydrated electron's equilibrium absorption, arises because the two electrons tend to separate in the excited state. In contrast, excitation of the hydrated electron gives a bleach signal in this wavelength region. Thus, our calculations suggest a clear pump-probe spectroscopic signature that may be used in the laboratory to distinguish hydrated singlet dielectrons from hydrated electrons: By choosing an excitation energy that is to the blue of the peak of the hydrated electron's absorption spectrum and probing near the maximum of the single electron's absorption, the single electron's transient bleach signal should shrink or even turn into a net absorption as sample conditions are varied to produce more dielectrons.