Kyungwon Kwak

Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: A new approach

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe structural dynamics under thermal equilibrium conditions on time scales ranging from femtoseconds to approximately 100 ps and longer. One of the important uses of 2D-IR spectroscopy is to monitor the dynamical evolution of a molecular system by reporting the time dependent frequency fluctuations of an ensemble of vibrational probes. The vibrational frequency-frequency correlation function (FFCF) is the connection between the experimental observables and the microscopic molecular dynamics and is thus the central object of interest in studying dynamics with 2D-IR vibrational echo spectroscopy. A new observable is presented that greatly simplifies the extraction of the FFCF from experimental data. The observable is the inverse of the center line slope (CLS) of the 2D spectrum. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first electric field-matter interaction. The CLS varies from a maximum of 1 to 0 as spectral diffusion proceeds. It is shown analytically to second order in time that the CLS is the T(w) (time between pulses 2 and 3) dependent part of the FFCF. The procedure to extract the FFCF from the CLS is described, and it is shown that the T(w) independent homogeneous contribution to the FFCF can also be recovered to yield the full FFCF. The method is demonstrated by extracting FFCFs from families of calculated 2D-IR spectra and the linear absorption spectra produced from known FFCFs. Sources and magnitudes of errors in the procedure are quantified, and it is shown that in most circumstances, they are negligible. It is also demonstrated that the CLS is essentially unaffected by Fourier filtering methods (apodization), which can significantly increase the efficiency of data acquisition and spectral resolution, when the apodization is applied along the axis used for obtaining the CLS and is symmetrical about tau=0. The CLS is also unchanged by finite pulse durations that broaden 2D spectra.

Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe the fast structural evolution of molecular systems under thermal equilibrium conditions. Structural dynamics are tracked by observing the time evolution of the 2D-IR spectrum, which is caused by frequency fluctuations of vibrational mode(s) excited during the experiment. However, there are a variety of effects that can produce line shape distortions and prevent the correct determination of the frequency-frequency correlation function (FFCF), which describes the frequency fluctuations and connects the experimental observables to a molecular level depiction of dynamics. In addition, it can be useful to analyze different parts of the 2D spectrum to determine if dynamics are different for subensembles of molecules that have different initial absorption frequencies in the inhomogeneously broadened absorption line. Here, an important extension to a theoretical method for extraction of the FFCF from 2D-IR spectra is described. The experimental observable is the center line slope (CLSomega(m)) of the 2D-IR spectrum. The CLSomega(m) is obtained by taking slices through the 2D spectrum parallel to the detection frequency axis (omega(m)). Each slice is a spectrum. The slope of the line connecting the frequencies of the maxima of the sliced spectra is the CLSomega(m). The change in slope of the CLSomega(m) as a function of time is directly related to the FFCF and can be used to obtain the complete FFCF. CLSomega(m) is immune to line shape distortions caused by destructive interference between bands arising from vibrational echo emission, from the 0-1 vibrational transition (positive), and from the 1-2 vibrational transition (negative) in the 2D-IR spectrum. The immunity to the destructive interference enables the CLSomega(m) method to compare different parts of the bands as well as comparing the 0-1 and 1-2 bands. Also, line shape distortions caused by solvent background absorption and finite pulse durations do not affect the determination of the FFCF with the CLSomega(m) method. The CLSomega(m) can also provide information on the cross correlation between frequency fluctuations of the 0-1 and 1-2 vibrational transitions.

Ultrafast Carbon-Carbon Single-Bond Rotational Isomerization in Room-Temperature Solution

Generally, rotational isomerization about the carbon-carbon single bond in simple ethane derivatives in room-temperature solution under thermal equilibrium conditions has been too fast to measure. We achieved this goal using two-dimensional infrared vibrational echo spectroscopy to observe isomerization between the gauche and trans conformations of an ethane derivative, 1-fluoro-2-isocyanato-ethane (1), in a CCl4 solution at room temperature. The isomerization time constant is 43 picoseconds (ps, 10–12 s). Based on this value and on density functional theory calculations of the barrier heights of 1, n-butane, and ethane, the time constants for n-butane and ethane internal rotation under the same conditions are ∼40 and ∼12 ps, respectively.

Direct observation of fast protein conformational switching.

Folded proteins can exist in multiple conformational substates. Each substate reflects a local minimum on the free-energy landscape with a distinct structure. By using ultrafast 2D-IR vibrational echo chemical-exchange spectroscopy, conformational switching between two well defined substates of a myoglobin mutant is observed on the ≈50-ps time scale. The conformational dynamics are directly measured through the growth of cross peaks in the 2D-IR spectra of CO bound to the heme active site. The conformational switching involves motion of the distal histidine/E helix that changes the location of the imidazole side group of the histidine. The exchange between substates changes the frequency of the CO, which is detected by the time dependence of the 2D-IR vibrational echo spectrum. These results demonstrate that interconversion between protein conformational substates can occur on very fast time scales. The implications for larger structural changes that occur on much longer time scales are discussed.

A Highly Planar Fluorinated Benzothiadiazole‐Based Conjugated Polymer for High‐Performance Organic Thin‐Film Transistors

High-mobility and low-voltage-operated organic field-effect transistors (OFETs) are demonstrated by the design of a new fluorinated benzothiadiazole-based conjugated polymer with fluorinated high-k polymer dielectrics. A record-breaking high hole mobility of 9.0 cm(2) V(-1) s(-1) for benzothiadiazole-based semiconducting polymers is achieved by the excellent planarity of the semiconducting polymer.

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

Neuroglobin (Ngb), a protein in the globin family, is found in vertebrate brains. It binds oxygen reversibly. Compared with myoglobin (Mb), the amino acid sequence has limited similarity, but key residues around the heme and the classical globin fold are conserved in Ngb. The CO adduct of Ngb displays two CO absorption bands in the IR spectrum, referred to as N3 (distal histidine in the pocket) and N0 (distal histidine swung out of the pocket), which have absorption spectra that are almost identical with the Mb mutants L29F and H64V, respectively. The Mb mutants mimic the heme pocket structures of the corresponding Ngb conformers. The equilibrium protein dynamics for the CO adduct of Ngb are investigated by using ultrafast 2D-IR vibrational echo spectroscopy by observing the CO vibrations spectral diffusion (2D-IR spectra time dependence) and comparing the results with those for the Mb mutants. Although the heme pocket structure and the CO FTIR peak positions of Ngb are similar to those of the mutant Mb proteins, the 2D-IR results demonstrate that the fast structural fluctuations of Ngb are significantly slower than those of the mutant Mbs. The results may also provide some insights into the nature of the energy landscape in the vicinity of the folded protein free energy minimum.

Disulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopy

Intramolecular disulfide bonds are understood to play a role in regulating protein stability and activity. Because disulfide bonds covalently link different components of a protein, they influence protein structure. However, the effects of disulfide bonds on fast (subpicosecond to ≈100 ps) protein equilibrium structural fluctuations have not been characterized experimentally. Here, ultrafast 2D-IR vibrational echo spectroscopy is used to examine the constraints an intramolecular disulfide bond places on the structural fluctuations of the protein neuroglobin (Ngb). Ngb is a globin family protein found in vertebrate brains that binds oxygen reversibly. Like myoglobin (Mb), Ngb has the classical globin fold and key residues around the heme are conserved. Furthermore, the heme-ligated CO vibrational spectra of Mb (Mb-CO) and Ngb (Ngb-CO) are virtually identical. However, in contrast to Mb, human Ngb has an intramolecular disulfide bond that affects its oxygen affinity and protein stability. By using 2D-IR vibrational echo spectroscopy, we investigated the equilibrium protein dynamics of Ngb-CO by observing the CO spectral diffusion (time dependence of the 2D-IR line shapes) with and without the disulfide bond. Despite the similarity of the linear FTIR spectra of Ngb-CO with and without the disulfide bond, 2D-IR measurements reveal that the equilibrium sampling of different protein configurations is accelerated by disruption of the disulfide bond. The observations indicate that the intramolecular disulfide bond in Ngb acts as an inhibitor of fast protein dynamics even though eliminating it does not produce significant conformational change in the proteins structure.

Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenols first solvent shell.

Vibrational interactions of acetonitrile: Doubly vibrationally resonant IR–IR–visible four-wave-mixing spectroscopy

The origin of the vibrational coupling that was observed between the CC and CN stretching modes of acetonitrile by doubly vibrationally enhanced (DOVE) IR–IR–Vis four-wave-mixing (IIV-FWM) spectroscopy is investigated by various ab initio calculations including DFT(B3LYP), HF, and MP2 methods with the same baisis set, 6-311++G**. The linear and nonlinear susceptibilities of the combination bands and cross peaks are numerically calculated and compared with the experimental values, and the agreement between ab initio results and experiments are quantitative. By separately analyzing the contributions from each coherence pathway to the vibrational coupling of the CC and CN stretching modes, a quantitative understanding of the DOVE IIV-FWM signals is possible. Although the direct coupling of the CC and CN stretching modes by mechanical and electric anharmonicity coupling is sizable, the CH bending and CH stretching modes are also involved in the vibrational coupling between CC and CN stretching modes as promot...

Nanoscopic Management of Molecular Packing and Orientation of Small Molecules by a Combination of Linear and Branched Alkyl Side Chains

We synthesized a series of acceptor-donor-acceptor-type small molecules (SIDPP-EE, SIDPP-EO, SIDPP-OE, and SIDPP-OO) consisting of a dithienosilole (SI) electron-donating moiety and two diketopyrrolopyrrole (DPP) electron-withdrawing moieties each bearing linear n-octyl (O) and/or branched 2-ethylhexyl (E) alkyl side chains. X-ray diffraction patterns revealed that SIDPP-EE and SIDPP-EO films were highly crystalline with pronounced edge-on orientation, whereas SIDPP-OE and SIDPP-OO films were less crystalline with a radial distribution of molecular orientations. Near-edge X-ray absorption fine structure spectroscopy disclosed an edge-on orientation with a molecular backbone tilt angle of ∼22° for both SIDPP-EE and SIDPP-EO. Our analysis of the molecular packing and orientation indicated that the shorter 2-ethylhexyl groups on the SI core promote tight π-π stacking of the molecular backbone, whereas n-octyl groups on the SI core hinder close π-π stacking to some degree. Conversely, the longer linear n-octyl groups on the DPP arms facilitate close intermolecular packing via octyl-octyl interdigitation. Quantum mechanics/molecular mechanics molecular dynamics simulations determined the optimal three-dimensional positions of the flexible alkyl side chains of the SI and DPP units, which elucidates the structural cause of the molecular packing and orientation explicitly. The alkyl-chain-dependent molecular stacking significantly affected the electrical properties of the molecular films. The edge-on oriented molecules showed high hole mobilities in organic field-effect transistors, while the radially oriented molecules exhibited high photovoltaic properties in organic photovoltaic cells. These results demonstrate that appropriate positioning of alkyl side chains can modulate crystallinity and molecular orientation in SIDPP films, which ultimately have a profound impact on carrier transport and photovoltaic performance.