Current research projects of Rubtsov Laboratory
1. Ballistic energy transport in molecules

NSF CHE-1462075, 2015-2018, NSF CHE-1900568 2019-2022

Understanding vibrational energy flow in molecules, resolved in time and space, is one of the challenges of physical chemistry. It is important for a wide range of fields, spanning from biochemistry, chemistry, and molecular electronics to novel materials and technology. In chemical reactions, vibrational energy of the reactants is required for reaching the transition state, whereas the removal of the excess energy from the products makes the reaction irreversible. Heat management problems occur in various areas of technology and science. Efficient removal of excess vibrational energy is crucial for the longevity of the elements for molecular electronics. Creating compact systems with controllable energy transport properties, including the cases of high, low, anisotropic, and controlled conductivities, is very desirable.


Earlier, Rubtsov group developed a new approach to 2DIR spectroscopy that uses vibrational energy transport in molecules to enhance the cross-peak amplitudes and therefore increase by several fold the range of distances experimentally accessible by 2DIR for structural measurements. The method is named relaxation-assisted 2DIR (RA 2DIR), see for example Acc. Chem. Res. (2009), and Proc. Natl. Acad. Sci. U.S.A., (2007) 104, 14209-14214. We have demonstrated that RA 2DIR can result in ca. 30-fold cross peak amplification and enables assessing distances up to 60Å. The RA 2DIR method is also suitable for assessing energy transport dynamics.


Heat transport in materials often occurs via acoustic phonons, low-frequency delocalized vibrational modes. Their delocalization greatly exceeds interatomic distances, allowing the formation of free propagating wavepackets. High-frequency modes in molecular materials, optical phonons, are typically much more localized than the acoustic modes, which limits their contribution to heat transport and prevents their use for efficient energy transport in such systems. However, energy transport through molecular backbones often occurs using high-frequency vibrations. Such vibrational modes can deliver much larger energy quanta. In addition, we found conditions at which such energy transport can be very fast and efficient, as proceeds in ballistic fashion. One can imagine a pack of energy (a wave packet) propagating via a molecular backbone at constant velocity. Moreover, the transport speed can be different within the same molecular chain depending on the transport initiation mechanism. Figure 1 summarizes results of the energy transport velocities via alkane chains.

Fig. 1. Energy transport speeds in alkane chains with initiation by azido-group excitation (blue and green), and carbonyl mode excitation (red). The chain bands responsible for the transport are indicated with matching color. [Rubtsova et al. Acc. Chem. Res., (2015), 48, 2547-2555;]


Current directions include studies of the transport via alien groups positioned in the middle of a regular chain (Fig. 2). Reformation of a vibrational wavepacket at the alien group and was recently observed (see Fig. 2 caption), which enables perturbing the transport and may permit its control via external stimuli.

Fig. 2. Results of energy transport via alien amide group positioned in the middle of a regular alkane chain. Reformation of a vibrational wavepacket at the amide is observed. [L. Qasim et al. J. Phys. Chem. C, (2019) 123(6) 3381;]

2. Infra-red control of electron transfer processes: implementation of a molecular interferometer.

NSF, CHE-1012371, 2010-2015; NSF CHE-1565427, 2016-2020

The project aims at investigating how to modulate (control) electron transfer pathways using mid-IR radiation and seeking an understanding of inelastic tunneling interactions in molecules. It is highly interdisciplinary project involving laboratories of experimental physical chemistry (us), inorganic/organic chemistry (laboratories of Profs. J. Sessler at UT Austin, R. Schmehl at Tulane, M. Therien at Duke, and Scott Hartley at Miami U. of Ohio) and theoretical chemistry (Prof. D. Beratan at Duke).


At the core of quantum mechanics is the notion of representing different possible outcomes by the coherent superposition of probability amplitudes (Scheme 1). In chemistry, coherent superpositions underlie chemical bonding, reactivity, and spectroscopy. These fundamental issues are particularly important for electron-transfer reactions. For example, nonadiabatic electron-transfer reactions involve the coherent tunneling of electron amplitude through a chemical “linker”. These tunneling reactions lie at the heart of solar energy conversion, bioenergetics, nanoscale information processing, and catalysis. We have recently discovered that IR excitation may be used to manipulate the propagation of electron amplitude from donor to acceptor species in molecules [J. Am. Chem. Soc. (2009), 131, 18060,] (Fig. 1). The objective of this research program is to explore new experimental and theoretical strategies that will enable the active control of electronic amplitude propagation in molecules through IR radiation.

Scheme 1. Electron transfer pathway interference in electron transfer between a donor and acceptor (right) is similarly important as interference in a double-slit-type experiment with electron (left).

Fig. 1. Examples of molecular systems interrogated for ET rate modulation with IR.


To study electron-transfer rate modulation we used a variety of experimental time-resolved ultrafast techniques such as three-pulse (UV or VIS) pump – mid-IR pump – (mid-IR or VIS) probe, UV-VIS transient absorption, (UV or VIS) pump – mid-IR probe, dual-frequency 2DIR, and triggered 2DIR spectroscopies.

New directions involve donor-acceptor compounds featuring rigid double-path bridges with tunable conjugation.

3. Structural assessment of thin films and molecular monolayers using surface-enhanced 2DIR with plasmonic nanoantenna arrays.

Binational Science Foundation grant 201667 with Prof. Lev Chuntonov at Technion, 2017-2021, and NSF MRI grant DMR-1727000, 2017-2020, with Prof. Matthew Escarra at Tulane for purchasing e-beam lithography instrument

Plasmonic nanoantenna arrays resonant with molecular transitions enable measuring minute quantities of sample due to signal enhancement provided by the array (Fig. 1). Such approach is widely used in linear spectroscopy in the visible spectral region and Raman spectroscopy. We have implemented such approaches for nonlinear IR spectroscopies (3rd-order in electric field - 2DIR - and 5th-order in electric field) [R. Mackin et al. J. Phys. Chem. C (2018) 122, 11015,; A. Gandman et al. ACS Nano, (2018) 12, 4521,].

Fig. 1. Characteristic sizes, signal enhancements and extinction spectra (FTIR) of a plasmonic array with and without sample. The nanoarrays were prepared using e-beam lithography.



Fig. 2. Cross-peak among NN and C=O modes of 1.0-nm-thick azNHS sample in polystyrene.



Fig. 3. 3rd-order 2DIR and 5th-order IR diagonal C=O peaks for 20-nm-thick azNHS sample in polystyrene (left) and mercaptoacetic acid monolayer (right).



Such strong enhancements permit measuring 2DIR spectra of molecular monolayers and investigate molecular structures and dynamics at interfaces (Fig. 2-3). By designing various antenna shapes, including gaps and trimers, stronger signal enhancements can be achieved, and the structure will enable resonance enhancements of several peaks at the same time permitting cross peak 2DIR measurements [R. Mackin et al. submitted to J. Phys. Chem. (2019)]. 


Strong field enhancement provided by the antennas permit creation of a vibrational population inversion. Four-fold population inversion between the total excited population and the ground state was for a molecular monolayer at low pump powers [R. Mackin et al. submitted to J. Chem. Phys. (2019)].

4. Development of a fully automated dual-frequency spectrometer for surface-enhanced ATR 2DIR studies

NSF MRI, CHE-1828531, 2018-2021

Processes at interfaces are vital for many fields of science including heterogeneous catalysis, sensing, recognition, molecular electronics and energy conversion and storage, and it is of great importance to development spectroscopic approaches for interrogating molecules at interfaces. We are developing a unique 2DIR spectrometer working in an attenuated total reflection (ATR) mode. The instrument sensitivity is enhanced by plasmonic nano-array attached to the ATR prism (see Figure). Dual-frequency capability will enable measuring any cross-peaks of choice within 1000-4000 cm-1 range. High-repetition rate (100 kHz) of the Ytterbium fs laser used helps increasing the sensitivity of the measurements.

5. Dynamics of the lipid membrane interior using vibrational spectroscopy.

Cell membranes perform many important functions in cell metabolism, including catalytic, structural, recognition, exchange, etc.  Cell membrane properties were linked to age related neurodegenerative disorders, such as Prion, Parkinson’s, and Alzheimer’s diseases. We are developing an approach to interrogate membrane properties, such as mobility, at various depths within a lipid membrane, which was not possible previously. We develop a test molecule featuring a linear alkyl chain terminated with an azido and cyano moieties to serve as vibrational reporter (Fig. 1, 4). We found that this compound orients itself in a membrane in such a way that the cyano group is located in the ester region of the lipids whereas the azido group is embedded into the membrane (Fig. 1), which makes it a convenient reporter of the interior mobility at specific depths. We used 2DIR spectral diffusion method (Fig. 2) to measure dynamics of the membrane.


We found that the spectral diffusion of N3-alkyl reflects the dynamics of the environment, even in the media of very low polarity [C. Varner et al. Chem. Phys. (2018) 512, 20-26;]. The membrane interior mobility was quantified (Fig. 3). The studies on the depth dependence of the mobility in membranes are in progress.



Fig. 1. Test compound capable of positioning N3 label at a specified depth within lipid membrane.




Fig. 2. Principles of the 2DIR spectral diffusion approach.



Fig. 3.  Mobility in lipid membrane interior at a depth of ca. 18 Å (in MLBL), compared to that of several solvents.


Fig. 4. Computed absorption spectrum of the azido-alkyl compound (N3- peak). Fermi resonances, dominated by VN=N fundamental and VN=N + VN-C combination band interaction, determine the width of the VN=N peak

6. Higher-order infrared spectroscopy – 5th-order 2DIR

Recently developed 3rd-order technique in the applied electric field, such as 2DIR spectroscopy, brought opportunities of measuring pair-wise vibrational mode interactions via cross peak detection. These advances enabled identifying molecular species which were masked for linear IR spectroscopy. Fifth-order techniques attracts high interest for structural determination as they provide even higher discrimination power. For example, multidimensional NMR spectroscopy, an additional dimension (3rd order vs. 5th order) offer over two orders of magnitude enhanced resolution, while a 3-fold increase in magnetic field, as for example associated with using a 900 MHz instrument instead of 300 MHz, results in just a 3-fold increase in spectral resolution.


Inspired by the advances of MD NMR spectroscopy to identify specific groups in a complicated sample based on 5th-order cross peaks (Fig. 1), we performed the first dual-frequency 5th-order spectroscopy measurements detecting 5th-order cross peaks between a variety of vibrational modes (Fig. 3) [J. Leger, et al. J. Chem. Phys. (2016), 145, 154201,]. Note that fully automated 2DIR instrument working in the transmission mode enable automatic switch between 3rd- and 5th- order peaks (Fig. 2). 


While it is challenging to measure 5th-order signals, we have demonstrated that with the current sensitivity of our 2DIR setup it is rather practical to measure such cross peaks among modes separated by over 600 cm-1 in frequency and ca. 12 Å in distance. As we recently showed plasmonic enhancement provided by gold nanoarrays offer an extremely strong field enhancement, thus making the 5th-order measurements even more practical.



Fig. 1. 5th-order cross peaks enable recognition enhancement. Here four vibrational probes in a molecule (L1-L3) are shown schematically. If the spectra of probes L2 and L2’ overlap, the 3rd-order cross peaks, L1/L2 and L1/L2’, overlap as well preventing discrimination between “left” and “right” sides of the molecule with respect to L1.  However, the 5th-order cross peak among L1, L2, and L3 will be much stronger than L1, L2’, and L3, thus permitting to recognize the “right” side of the molecule.



Fig. 2. Schematics of the laser beam directions that satisfy the phase-matching conditions for the 3rd-order, and 5th-order cross peaks. Fast switching between the two geometries is achieved. n(C=O)/n(CNC) and n(C=O),n(C=O)/n(CNC) cross peaks measured for the azNHS sample under the beam geometry optimal for the (c) 3rd-order and (d) 5th-order signals. For both measurements the k1 and k3 beams were centered at 1750 and 1208 cm-1, respectively.




Fig. 3. a) Absorptive 5th-order spectrum involving two-quantum excitation of the carbonyl modes of azNHS and single excitation of CNC stretching mode at 1208 cm-1. Center-line slopes are shown for six peaks (black and red lines). Normalized projections onto the wt axis (black lines) for individual peaks integrated over wt within the indicated boxes and their fits (red) are shown in panels b) and c).

7. Molecular interactions of Aβ peptides (Alzheimer disease peptides).

Alzheimer disease (AD) causes brain dementia and is the third leading cause of death in the United States. While the origin of AD is unknown, there exist many hypotheses. Cell membrane plays an important role in AD.  The project accesses experimentally the properties of cell membranes using specially developed 2DIR probes capable of probing cell membranes at any required depth. Influence of membrane composition and membrane proteins onto the membrane properties are investigated. Cleavage of Alzheimer precursor peptide (APP), releasing Aβ peptides (Figure), and following metabolism of the peptides are considered crucial for the Alzheimer disease. APP is a transmembrane protein; its conformation depends on the properties of the cell membrane. Interactions of Aβ peptides and enzymes such as IDE (Insulin degrading enzyme) are also targeted.






Available Research Equipment
1. Unique fully automated dual-frequency 2DIR instrument

Built with support from NSF MRI, instrument development grant, CHE-1040491 and Louisiana Board of Regents grant LEQSF(2011-12)-ENH-TR-29, 2011-2013

Two-dimensional infrared (2DIR) spectroscopy emerged about two decades ago as a new tool for measuring three-dimensional structures of molecules in solution and in solid phase. The method enables measuring pair-wise interaction strengths (couplings) of vibrational modes in molecules – the coupling strength reports on the distance between the vibrating groups, thus providing a bit of structural information on the molecule. The coupling is determined from the amplitude of the cross-peak in the 2DIR spectrum; by combining many bits of structural data the 3D structure of the molecule can be determined. Many vibrational modes in molecules are localized on particular groups, which make them perfect reporters for the molecular structure. The power of 2DIR spectroscopy has been demonstrated on numerous examples, including drugs, peptides, transition metal complexes, and recently proteins. Wider implementation of this powerful method is constricted by the 2DIR instrument development. The Rubtsov group at Tulane developed the first fully automated dual-frequency 2DIR instrument, which features unprecedented sensitivity. The instrument permits measuring cross peak between any modes within a spectral range from 800 to 4000 cm-1. The sensitivity is reaching 10-4 cm-1 – if excitation of one vibrational mode changes the frequency of another mode by 10-4 cm-1, such weak interaction can be observed. The principle (Fig. 1) and detailed (Fig. 2) schematics of the instrument are shown.



Fig. 1. Principle schematic of the instrument.


Fig. 2.  Detailed schematic of the instrument [J. Leger et al. Rev. Sci. Instr., (2014) 85, 083109-16,;  C. Nyby et al. Opt. Express, (2014), 22 (6), 6801-6809,].

2. Three-pulse UV-VIS – Mid-IR – VIS-mid-IR transient spectroscopy

This setup enables measuring how the dynamics of the excited state formed by UV-VIS excitation can be modulated by vibrational; excitation in mid-IR (Fig. 1). The detection can be performed at a wide range of wavelength from VIS to mid-IR.



Fig. 1.  Experimental setup for three-pulse spectroscopy (left) and experimental pulse sequence (right).


The setup also permits measuring 2-pulse transient absorption spectra. An example of transient IR spectra followed 402 nm excitation is shown in Fig. 2 for the compound shown in Scheme 1.





















Fig. 2. Transient infrared spectrum of ReEBA (Fig. 3) in DCM following 402 nm excitation at selected time delays. Insets show kinetics measured at indicated frequencies and their fits to single or double exponential functions. [Yue, Y. et al. J. Phys. Chem. A (2014) 118, 10407-10415;]















Scheme 1.

3. Surface-enhanced ATR 2DIR spectroscopy.

The instrument for surface-enhanced 2DIR measurements is under construction. It will permit measuring 2DIR spectra of nm-thick layers and molecular monolayers.

4. Other equipment

The lab hosts a large arsenal of scientific equipment, including

optical closed-loop helium cryostat capable of reaching temperatures down t o10K;

vacuum station;

spin coating setup;

ultra sonicator;


press and die sets for making solid films;



Tulane clean room offers a variety of equipment, such as spattering, e-beam lithography, AFM/STM, to name those used actively by the group.


Two FTIR spectrometers (Bruker and Thermo-Nicolet) and an ultracentrifuge are accessible at the Department of Chemistry.


The Rubtsov lab hosts a Linux computer cluster, which is used predominantly for quantum-chemistry DFT calculation using Gaussian suite.