Solvent-dependent structural dynamics of an azido-platinum complex revealed by linear and nonlinear infrared spectroscopy

MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe

Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.

Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy

There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.

Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (^TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.

Ultrafast Structure and Vibrational Dynamics of a Cyano-Containing Non-Fullerene Acceptor for Organic Solar Cells Revealed by Two-Dimensional Infrared Spectroscopy

Non-fullerene molecules, such as ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene) indanone)-5,5,11,11-tetrakis(4-hexylphenyl)dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), are among the most promising non-fullerene acceptors for organic solar cells (OSCs). In this work, using the cyano stretching mode as a vibrational marker, the structural and vibrational energy dynamics of ITIC were examined on an ultrafast time scale with two-dimensional infrared spectroscopy. Two IR-active modes studied here mainly correspond to two anti-symmetric combinations of symmetric and asymmetric stretching vibrations of two C≡N modes originating from two -C(CN)₂ chromophores that are located across the ITIC system, which were found to have significantly larger off-diagonal anharmonicity than their corresponding diagonal anharmonicities. This indicates strong anharmonic vibrational coupling between the two modes, which is supported by ab initio anharmonic frequency computations. Transient IR results indicate picosecond intramolecular vibrational energy transfer between the two C≡N modes upon excitation. The structural basis for these vibrational and energetic features is the conjugating molecular frame that is composed of a network of single/double bonds connecting the two -C(CN)₂ chromophores and may enable efficient vibration delocalization, in addition to its well-known electron delocalization capability. The importance of the results for the OSC applications is discussed.

Excited-state photophysical processes in a molecular system containing perylene bisimide and zinc porphyrin chromophores

Multichromophoric systems with efficient photoinduced excited-state processes are important for the conversion of solar energy in artificial photosynthesis. However, a low molecular absorption coefficient of these multichromophoric systems in the near-infrared region limits their power conversion efficiency in organic solar cells. It is critical to design molecules with a broad absorption range in the whole spectral region, to better harvest solar energy, and to reveal their important multiple-step photophysical processes for the design of organic solar cells. Here, we investigate a novel compound having three chromophores, namely two near-by N,N'-bis(1-pentyl)hexyl-3,4,9,10-perylenebiscarboximide (PDI) units linked to a zinc porphyrin core side by side (in the form of PDI-ZnPor-PDI), which absorbs solar energy ranging from the ultraviolet (UV) to near-infrared regions. The photophysical behavior of PDI-ZnPor-PDI in both film and solution forms, has been investigated using steady-state and transient spectroscopy measurements. Charge-transfer species and triplet excited-state species are observed, the excited-state evolutions of which are monitored using molecular vibrations as probes. These observations support the idea that PDI-ZnPor-PDI on photoexcitation generates the radical anion and triplet species of the PDI unit (PDI˙- and 3PDI*). Our results demonstrate the effect of solid film state on the photophysical properties in such multichromophoric system, and are valuable for guiding the design and utilization of novel near-infrared electron donors or acceptors for use in organic solar cells.

Ultrafast Vibrational Energy Transfer through the Covalent Bond and Intra- and Intermolecular Hydrogen Bonds in a Supramolecular Dimer by Two-Dimensional Infrared Spectroscopy

In this work, the structural fluctuations and vibrational energy transfer dynamics in a supramolecular homodimer model, which is composed of 2-(9-anthracene)ureido-6-(1-undecyl)-4[1H]-pyrimidinone (UPAn) with quadruple intermolecular and single intramolecular hydrogen bonds (HBs), have been examined using ultrafast two-dimensional infrared (2D IR) and steady-state IR spectroscopies. A less structurally fluctuating intermolecular HB is found between the pyrimidinone C═O and ureido N-H groups. However, a larger structurally fluctuating intramolecular HB is suggested by the equilibrium and dynamical line-shape measurements of the ureido C═O stretch. Further, dynamical time-dependent 2D IR diagonal and off-diagonal signals show that intra- and intermolecular vibrational energy transfer processes occur on the picosecond timescale, where the latter is more efficient due to intermolecular hydrogen bonding interaction and through-space interaction.

Two-dimensional infrared spectral explorations into bilayer and monolayer self-assemblies of amphiphilic polypeptides

Poly(2-(3-((2-hydroxyethyl)amino)-3-oxopropyl)ethyleneamido) (PHAOE) is an amphiphilic polypeptide. The self-assembly is significant, but the ultrafast dynamic analyses of the peptide self-assembly are exiguous and worth further exploring. In this investigation, the temporal dynamic characteristics of the aggregates and unaggregated PHAOEs are mined by the two-dimensional infrared (2D IR) spectroscopy. The homogeneous and inhomogeneous diffusion processes of the carbonyl stretching modes of the unaggregated PHAOEs are slower than those of the self-assemblies. The inhomogeneous spectral diffusion proportion of the biopolymer PHAOE in methanol is greater than that in dimethyl sulfoxide (DMSO). The solvation shells surround the aggregates and unaggregated PHAOEs in the protic solvent methanol, but there are not any solvation shells around the aggregates or unaggregated PHAOEs in the dipolar solvent DMSO. The massive hydrogen-bonded monolayer self-assembly has merely an aggregate of PHAOEs and no solvation shell in DMSO. But the hydrogen-bonded bilayer self-assembly has a self-assembled methanol shell and an interior aggregate of PHAOEs in methanol. The self-assemblies of PHAOEs motivate the methanols to self-assemble. The large delocalized amide structure results in the fast spectral diffusion of the carbonyl stretching mode.Communicated by Ramaswamy H. Sarma.

Ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two-dimensional infrared spectroscopy

In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear infrared and nonlinear two-dimensional infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these delocalized C=N stretching modes, acting as an efficient vibrational energy transfer channel. This work reasonably connects the experimentally observed IR signature to a specific g-CN structure and also provides the first report on the ultrafast intramolecular processes of such carbon nitride systems. The obtained results are fundamentally important for understanding the molecular mechanisms of such carbon-nitride based functional materials.

Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution

In this work, the solvation of a nitrosyl ruthenium complex, [(CH₃)₄N][RuCl₃(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D₂O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D₂O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D₂O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D₂O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.