Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy

Modulating vibrational energy redistribution in highly conjugated systems

Elucidating the nature of intramolecular vibrational energy redistribution (IVR) can guide the design of molecular wires. The ability to steer these processes through a mechanistic understanding of IVR is assessed by utilizing two-dimensional infrared (2D IR) spectroscopy. 2D IR spectroscopy allows for the direct investigation of timescales of energy transfer within three aromatic molecular scaffolds: 4'-azido-[1,1'-biphenyl]-4-carbonitrile (PAB), 2'-azido-[1,1'-biphenyl]-4-carbonitrile (OAB), and 4'-(azidomethyl)-[1,1'-biphenyl]-4-carbonitrile (PAMB). Energy transfer pathways between azido (N3)- and cyano (CN)-vibrational reporters uncover the importance of Fermi resonances, anharmonic coupling, and specific structural components in directing energy flow. Among these systems, PAB exhibits the fastest energy transfer (22 ps), facilitated by its co-planar biphenyl structure, enabling strong π-π stacking interactions to optimize vibrational coupling. In contrast, OAB demonstrates a moderate IVR timescale (38 ps) due to an orthogonal molecular plane and steric hindrance, which disrupts coupling pathways. PAMB, with a para-methylene group, introduces a structural bottleneck that significantly impedes energy flow, slowing down the energy transfer to 84 ps. The observed IVR rates align with computational predictions, highlighting intermediate ring modes in PAB as efficient energy transfer bridges, a mechanism that is less pronounced in OAB and PAMB. This study demonstrates that IVR is dictated not only by anharmonic coupling strengths but also by the extended alignment of vibrational modes across molecular planes and their delocalization within aromatic scaffolds. By modulating structural features, such as steric constraints and π-π interactions, we provide a framework for tailoring energy flow in conjugated molecular systems. These findings offer new insights into IVR dynamics for applications in molecular electronics.

Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein

Proteins that do not fold into their functional native state have been linked to diseases. In this study, the influence of the main and side chains of individual amino acids on the folding of the tryptophan cage (Trp-cage), a designed 20-residue miniprotein, was analyzed. For this purpose, we calculated the solvation free energy (SFE) contributions of individual atoms by using the 3D-reference interaction site model with the atomic decomposition method. The mechanism by which the Trp-cage is stabilized during the folding process was examined by calculating the total energy, which is the sum of the conformational energy and SFE. The folding process of the Trp-cage resulted in a stable native state, with a total energy that was 62.4 kcal/mol lower than that of the unfolded state. The solvation entropy, which is considered to be responsible for the hydrophobic effect, contributed 31.3 kcal/mol to structural stabilization. In other words, the contribution of the solvation entropy accounted for approximately half of the total contribution to Trp-cage folding. The hydrophobic core centered on Trp6 contributed 15.6 kcal/mol to the total energy, whereas the solvation entropy contribution was 6.3 kcal/mol. The salt bridge formed by the hydrophilic side chains of Asp9 and Arg16 contributed 10.9 and 5.0 kcal/mol, respectively. This indicates that not only the hydrophobic core but also the salt bridge of the hydrophilic side chains gain solvation entropy and contribute to stabilizing the native structure of the Trp-cage.

An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package

Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. In this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.

Inhibition of vibrational energy flow within an aromatic scaffold via heavy atom effect

The regulation of intramolecular vibrational energy redistribution (IVR) to influence energy flow within molecular scaffolds provides a way to steer fundamental processes of chemistry, such as chemical reactivity in proteins and design of molecular diodes. Using two-dimensional infrared (2D IR) spectroscopy, changes in the intensity of vibrational cross-peaks are often used to evaluate different energy transfer pathways present in small molecules. Previous 2D IR studies of para-azidobenzonitrile (PAB) demonstrated that several possible energy pathways from the N3 to the cyano-vibrational reporters were modulated by Fermi resonance, followed by energy relaxation into the solvent [Schmitz et al., J. Phys. Chem. A 123, 10571 (2019)]. In this work, the mechanisms of IVR were hindered via the introduction of a heavy atom, selenium, into the molecular scaffold. This effectively eliminated the energy transfer pathway and resulted in the dissipation of the energy into the bath and direct dipole-dipole coupling between the two vibrational reporters. Several structural variations of the aforementioned molecular scaffold were employed to assess how each interrupted the energy transfer pathways, and the evolution of 2D IR cross-peaks was measured to assess the changes in the energy flow. By eliminating the energy transfer pathways through isolation of specific vibrational transitions, through-space vibrational coupling between an azido (N3) and a selenocyanato (SeCN) probe is facilitated and observed for the first time. Thus, the rectification of this molecular circuitry is accomplished through the inhibition of energy flow using heavy atoms to suppress the anharmonic coupling and, instead, favor a vibrational coupling pathway.

Molecular Vibrational Polariton Dynamics: What Can Polaritons Do?

ConspectusWhen molecular vibrational modes strongly couple to virtual states of photonic modes, new molecular vibrational polariton states are formed, along with a large population of dark reservoir modes. The polaritons are much like the bonding and antibonding molecular orbitals when atomic orbitals form molecular bonds, while the dark modes are like nonbonding orbitals. Because the polariton states are half-matter and half-light, whose energy is shifted from the parental states, polaritons are predicted to modify chemistry under thermally activated conditions, leading to an exciting and emerging field known as polariton chemistry that could potentially shift paradigms in chemistry. Despite several published results supporting this concept, the chemical physics and mechanism of polariton chemistry remain elusive. One reason for this challenge is that previous works cannot differentiate polaritons from dark modes. This limitation makes delineating the contributions to chemistry from polaritons and dark states difficult. However, this level of insight is critical for developing a solid mechanism for polariton chemistry to design and predict the outcome of strong coupling with any given reaction. My group addressed the challenge of differentiating the dynamics of polaritons and dark modes by ultrafast two-dimensional infrared (2D IR) spectroscopy. Specifically, (1) we found that polaritons can facilitate intra- and intermolecular vibrational energy transfer, opening a pathway to control vibrational energy flow in liquid-phase molecular systems, and (2) by studying a single-step isomerization event, we verified that indeed polaritons can modify chemical dynamics under strong coupling conditions, but in contrast, the dark modes behave like uncoupled molecules and do not change the dynamics. This finding confirmed the central concept of polariton chemistry: polaritons modify the potential energy landscape of reactions. The result also clarified the role of dark modes, which lays a critical foundation for designing cavities for future polariton chemistry. Aside from using 2D IR spectroscopy to study polariton chemistry, we also used the same technique to develop molecular polaritons into a potential quantum simulation platform. We demonstrated that polaritons have Rabi oscillations, and using a checkerboard cavity design, we showed that polaritons could have large nonlinearity across space. We further used the checkerboard polaritons to simulate coherence transfer and visualize it. A unidirectional coherence transfer was observed, indicating non-Hermitian dynamics. The highlighted efforts in this Account provide a solid understanding of the capability of polaritons for chemistry and quantum information science. I conclude this Account by discussing a few challenges for moving polariton chemistry toward being predictable and making the polariton quantum platform a complement to existing systems.

Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics

Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy minima. In this paper, a new method of this kind is proposed in which the well-sliced metadynamics approach (WSMTD) is united with replica exchange with solute tempering (REST2) method. WSMTD employs a divide-and-conquer strategy wherein high-dimensional slices of a free energy surface are independently sampled and combined. The method enables one to accomplish a controlled exploration of the CV-space with a restraining bias as in umbrella sampling, and enhance-sampling of one or more orthogonal CVs using a metadynamics like bias. The new hybrid method proposed here enables boosting the sampling of more slow degrees of freedom in WSMTD simulations, without the need to specify associated CVs, through a replica exchange scheme within the framework of REST2. The high-dimensional slices of the probability distributions of CVs computed from the united WSMTD and REST2 simulations are subsequently combined using the weighted histogram analysis method to obtain the free energy surface. We show that the new method proposed here is accurate, improves the conformational sampling, and achieves quick convergence in free energy estimates. We demonstrate this by computing the conformational free energy landscapes of solvated alanine tripeptide and Trp-cage mini protein in explicit water.

Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy

Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm^-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.

Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant

The replica-exchange Monte Carlo method based on the single amino acid potential (SAAP) force field, i.e., REMC/SAAP3D, was recently developed by our group for the molecular simulation of short peptides. In this study, the method has been improved by applying a distance-dependent dielectric (DDD) constant and extended to the peptides containing D-amino acid (AA) residues. For chignolin (10 AAs), a sigmoidal DDD model reasonably allocated the native-like β-hairpin structure with all-atom root mean square deviation (RMSD) = 2.0 Å as a global energy minimum. The optimal DDD condition was subsequently applied for Trp-cage (20 AAs) and its G10q mutant. The native-like α-rich folded structures with main-chain RMSD = 3.7 and 3.8 Å were obtained as global energy minima for Trp-cage and G10q, respectively. The results suggested that the REMC/SAAP3D method with the sigmoidal DDD model is useful for structural prediction for the short peptides comprised of up to 20 AAs. In addition, the relative contributions of SAAP to the total energy (%SAAP) were evaluated by energetic component analysis. The ratios of %SAAP were about 40 and 20% for chignolin and Trp-cage (or G10q), respectively. It was proposed that SAAP is more important for the secondary structure formation than for the assembly to a higher-order folded structure, in which the attractive van der Waals interaction may play a more important role.

Extending the vibrational lifetime of azides with heavy atoms

The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.