Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines.

Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (µ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.

Characterizing Mode Anharmonicity and Huang-Rhys Factors Using Models of Femtosecond Coherence Spectra.

Femtosecond laser pulses readily produce coherent quantum beats in transient-absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck-Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang-Rhys factors and anharmonicity values. We discuss the extracted Huang-Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from molecular vibrations, which will aid studies of molecular aggregates and photosynthetic proteins.

Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions.

Biliproteins are a unique class of photosynthetic proteins in their diverse, and at times, divergent biophysical function. The two contexts of photosynthetic light harvesting and photoreception demonstrate characteristically opposite criteria for success, with light harvesting demanding structurally-rigid chromophores which minimize excitation quenching, and photoreception requiring structural flexibility to enable conformational isomerization. The functional plasticity borne out in these two biological contexts is a consequence of the structural plasticity of the pigments utilized by biliproteins-linear tetrapyrroles, or bilins. In this work, the intrinsic flexibility of the bilin framework is investigated in a bottom-up fashion by reducing the active nuclear degrees of freedom through model dipyrrole subunits of the bilin core and terminus free of external protein interactions. Steady-state spectroscopy was carried out on the dipyrrole (DPY) and dipyrrinone (DPN) subunits free in solution to characterize their intrinsic spectroscopic properties including absorption strengths and nonradiative activity. Transient absorption (TA) spectroscopy was utilized to determine the mechanism and kinetics of nonradiative decay of the dipyrrole subunits, revealing dynamics dominated by rapid internal conversion with some Z→E isomerization observable in DPY. Computational analysis of the ground state conformational landscapes indicates enhanced complexity in the asymmetric terminal subunit, and the prediction was confirmed by heterogeneity of species and kinetics observed in TA. Taken together, the large oscillator strengths (f ∼ 0.6) of the dipyrrolic derivatives and chemically-efficient spectral tunability seen through the ∼100 nm difference in absorption spectra, validate Nature's "selection" of multi-pyrrole pigments for light capture applications. However, the rapid deactivation of the excited state via their natural torsional activity when free in solution would limit their effective biological function. Comparison with phytochrome and phycocyanin 645 crystal structures reveals binding motifs within the in vivo bilin environment that help to facilitate or inhibit specific inter-pyrrole twisting vital for protein operation.

Revealing structural involvement of chromophores in algal light harvesting complexes using symmetry-adapted perturbation theory.

The attribution of quantum beats observed in the time-resolved spectroscopy of photosynthetic light-harvesting antennae to nontrivial quantum coherences has sparked a flurry of research activity beginning a decade ago. Even though investigations into the functional aspects of photosynthetic light-harvesting were supported by X-ray crystal structures, the non-covalent interactions between pigments and their local protein environment that drive such function has yet to be comprehensively explored. Using symmetry-adapted perturbation theory (SAPT), we have comprehensively determined the magnitude and compositions of these non-covalent interactions involving light-harvesting chromophores in two quintessential photosynthetic pigment-protein complexes - peridinin chlorophyll-a protein (PCP) from dinoflagellate Amphidinium carterae and phycocyanin 645 (PC645) from cryptophyte Chroomonas mesostigmatica. In PCP, the chlorophylls are dispersion-bound to the peridinins, which in turn are electrostatically anchored to the protein scaffold via their polar terminal rings. This might be an evolutionary design principle in which the relative orientation of the carotenoids towards the aqueous environment determines the arrangement of the other chromophores in carotenoid-based antennas. On the other hand, electrostatics dominate the non-covalent interactions in PC645. Our ab initio simulations also suggest full protonation of the PC645 chromophores in physiological conditions, and that changes to their protonation states result in their participation as switches between folded and unfolded conformations.

High Magnetic Field Detunes Vibronic Resonances in Photosynthetic Light Harvesting.

The origin and role of oscillatory features detected in recent femtosecond spectroscopy experiments of photosynthetic complexes remain elusive. A key hypothesis underneath of these observations relies on electronic-vibrational resonance, where vibrational levels of an acceptor chromophore match the donor-acceptor electronic gap, accelerating the downhill energy transfer. Here we identify and detune such vibronic resonances using a high magnetic field that exclusively shifts molecular exciton states. We implemented ultrafast pump-probe spectroscopy into a specialized 25 T magnetic field facility and studied the light-harvesting complex PC645 from a cryptophyte algae where strongly coupled chromophores form molecular exciton states. We detected a change in high-frequency coherent oscillations when the field was engaged. Quantum chemical calculations coupled with a vibronic model explain the experiment as a magnetic field-induced shift of the exciton states, which in turn affects the electronic-vibrational resonance between pigments within the protein. Our results demonstrate the delicate sensitivity of interpigment coherent oscillations of vibronic origin to electronic-vibrational resonance interactions in light-harvesting complexes.

Striking the right balance of intermolecular coupling for high-efficiency singlet fission.

Singlet fission is a process that splits collective excitations, or excitons, into two with unity efficiency. This exciton splitting process, unique to molecular photophysics, has the potential to considerably improve the efficiency of optoelectronic devices through more efficient light harvesting. While the first step of singlet fission has been characterized in great detail, subsequent steps critical to achieving overall highly-efficient singlet-to-triplet conversion are only just beginning to become well understood. One of the most elementary suggestions, which has yet to be tested, is that an appropriately balanced coupling is necessary to ensure overall highly efficient singlet fission; that is, the coupling needs to be strong enough so that the first step is fast and efficient, yet weak enough to ensure the independent behavior of the resultant triplets. In this work, we show how high overall singlet-to-triplet conversion efficiencies can be achieved in singlet fission by ensuring that the triplets comprising the triplet pair behave as independently as possible. We show that side chain sterics govern local packing in amorphous pentacene derivative nanoparticles, and that this in turn controls both the rate at which triplet pairs form and the rate at which they decay. We show how compact side chains and stronger couplings promote a triplet pair that effectively couples to the ground state, whereas bulkier side chains promote a triplet pair that appears more like two independent and long-lived triplet excitations. Our results show that the triplet pair is not emissive, that its decay is best viewed as internal conversion rather than triplet-triplet annihilation, and perhaps most critically that, in contrast to a number of recent suggestions, the triplets comprising the initially formed triplet pair cannot be considered independently. This work represents a significant step toward better understanding intermediates in singlet fission, and how molecular packing and couplings govern overall triplet yields.

Coherence Spectroscopy in the Condensed Phase: Insights into Molecular Structure, Environment, and Interactions.

The role of coherences, or coherently excited superposition states, in complex condensed-phase systems has been the topic of intense interest and debate for a number of years. In many cases, coherences have been utilized as spectators of ultrafast dynamics or for identifying couplings between electronic states. In rare cases, they have been found to drive excited state dynamics directly. Interestingly though, the utilization of coherences as a tool for high-detail vibronic spectroscopy has largely been overlooked until recently, despite their encoding of key information regarding molecular structure, electronically sensitive vibrational modes, and intermolecular interactions. Furthermore, their detection in the time domain makes for a highly comprehensive spectroscopic technique wherein the phase and dephasing times are extracted in addition to amplitude and intensity, an element not afforded in analogous frequency domain "steady-state" measurements. However, practical limitations arise in disentangling the large number of coherent signals typically accessed in broadband nonlinear spectroscopic experiments, often complicating assignment of the origin and type of coherences generated. Two-dimensional electronic spectroscopy (2DES) affords an avenue by which to disperse and decompose the large number of coherent signals generated in nonlinear experiments, facilitating the assignment of various types of quantum coherences. 2DES takes advantage of the broad bandwidth necessary for achieving the high time resolution desired for ultrafast dynamics and coherence generation by resolving the excitation axis to detect all excitation channels independently. This feature is beneficial for following population dynamics such as electronic energy transfer, and 2DES has become the choice method for such studies. Simultaneously, coherences arise as oscillations at well-defined coordinates across the 2D map often atop those evolving population signals. By isolating the coherent contribution to the 2DES data and Fourier transforming along the population time, a 3D spectral representation of the coherent 2D data is generated, and coherences are then ordered by their oscillation frequency, ν2. Individual coherences can then be selected by their frequency and evaluated via their distinct "2D coherence" spectra, yielding a significantly more distinctive set of spectroscopic signatures over other 1D methodologies and single-point 2DES analysis. Given that coherences of different origin result in unique 2D coherence spectra, these characteristics can be catalogued and compared directly against experiment for prompt assignment, a strategy not afforded by traditional 2DES analysis. In this Account, a structure-driven time-independent spectral model is discussed and employed to compare the 2D fingerprints of various coherences to experimental 2D coherence spectra. The frequency-domain approach can easily integrate ab initio derived vibronic parameters, and its correspondence with experimental coherence spectra of a model compound is demonstrated. Several examples and applications are discussed herein, from 2D Franck-Condon analysis of a model compound, to identifying the signatures of interpigment vibronic coupling in a photosynthetic light-harvesting complex. The 3D spectral approach to 2DES provides remarkable spectroscopic detail, in turn leading to new insights in molecular structure and interactions, which complement the time-resolved dynamics simultaneously recorded. The approach presented herein has the potential to distill down the convoluted set of nonlinear signals appearing in 2D coherent spectra, making the technique more amenable to high-detail vibronic spectroscopy in inherently complex condensed phase systems.

Tuning Singlet Fission in π-Bridge-π Chromophores.

We have designed a series of pentacene dimers separated by homoconjugated or nonconjugated bridges that exhibit fast and efficient intramolecular singlet exciton fission (iSF). These materials are distinctive among reported iSF compounds because they exist in the unexplored regime of close spatial proximity but weak electronic coupling between the singlet exciton and triplet pair states. Using transient absorption spectroscopy to investigate photophysics in these molecules, we find that homoconjugated dimers display desirable excited-state dynamics, with significantly reduced recombination rates as compared to conjugated dimers with similar singlet fission rates. In addition, unlike conjugated dimers, the time constants for singlet fission are relatively insensitive to the interplanar angle between chromophores, since rotation about σ bonds negligibly affects the orbital overlap within the π-bonding network. In the nonconjugated dimer, where the iSF occurs with a time constant >10 ns, comparable to the fluorescence lifetime, we used electron spin resonance spectroscopy to unequivocally establish the formation of triplet-triplet multiexcitons and uncoupled triplet excitons through singlet fission. Together, these studies enable us to articulate the role of the conjugation motif in iSF.

Photophysical characterization and time-resolved spectroscopy of a anthradithiophene dimer: exploring the role of conformation in singlet fission.

Quantitative singlet fission has been observed for a variety of acene derivatives such as tetracene and pentacene, and efforts to extend the library of singlet fission compounds is of current interest. Preliminary calculations suggest anthradithiophenes exhibit significant exothermicity between the first optically-allowed singlet state, S1, and 2 × T1 with an energy difference of >5000 cm-1. Given the fulfillment of this ingredient for singlet fission, here we investigate the singlet fission capability of a difluorinated anthradithiophene dimer (2ADT) covalently linked by a (dimethylsilyl)ethane bridge and derivatized by triisobutylsilylethynyl (TIBS) groups. Photophysical characterization of 2ADT and the single functionalized ADT monomer were carried out in toluene and acetone solution via absorption and fluorescence spectroscopy, and their photo-initiated dynamics were investigated with time-resolved fluorescence (TRF) and transient absorption (TA) spectroscopy. In accordance with computational predictions, two conformers of 2ADT were observed via fluorescence spectroscopy and were assigned to structures with the ADT cores trans or cis to one another about the covalent bridge. The two conformers exhibited markedly different excited state deactivation mechanisms, with the minor trans population being representative of the ADT monomer showing primarily radiative decay, while the dominant cis population underwent relaxation into an excimer geometry before internally converting to the ground state. The excimer formation kinetics were found to be solvent dependent, yielding time constants of ∼1.75 ns in toluene, and ∼600 ps in acetone. While the difference in rates elicits a role for the solvent in stabilizing the excimer structure, the rate is still decidedly long compared to most singlet fission rates of analogous dimers, suggesting that the excimer is neither a kinetic nor a thermodynamic trap, yet singlet fission was still not observed. The result highlights the sensitivity of the electronic coupling element between the singlet and correlated triplet pair states, to the dimer conformation in dictating singlet fission efficiency even when the energetic requirements are met.

Cooperative Subunit Refolding of a Light-Harvesting Protein through a Self-Chaperone Mechanism.

The fold of a protein is encoded by its amino acid sequence, but how complex multimeric proteins fold and assemble into functional quaternary structures remains unclear. Here we show that two structurally different phycobiliproteins refold and reassemble in a cooperative manner from their unfolded polypeptide subunits, without biological chaperones. Refolding was confirmed by ultrafast broadband transient absorption and two-dimensional electronic spectroscopy to probe internal chromophores as a marker of quaternary structure. Our results demonstrate a cooperative, self-chaperone refolding mechanism, whereby the ß-subunits independently refold, thereby templating the folding of the α-subunits, which then chaperone the assembly of the native complex, quantitatively returning all coherences. Our results indicate that subunit self-chaperoning is a robust mechanism for heteromeric protein folding and assembly that could also be applied in self-assembled synthetic hierarchical systems.

Broad-Band Pump-Probe Spectroscopy Quantifies Ultrafast Solvation Dynamics of Proteins and Molecules.

In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.

Ultrafast transient absorption revisited: Phase-flips, spectral fingers, and other dynamical features.

We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from the optical response of an individual molecule to incident femtosecond pump and probe pulses. The resulting description makes use of pulse propagators and free molecular evolution operators to arrive at compact expressions for the several contributions to a transient-absorption signal. In this alternative description, which is physically equivalent to the conventional response-function formalism, these signal contributions are conveniently expressed as quantum mechanical overlaps between nuclear wave packets that have undergone different sequences of pulse-driven optical transitions and time-evolution on different electronic potential-energy surfaces. Using this setup in application to a simple, multimode model of the light-harvesting chromophores of PC577, we develop wave-packet pictures of certain generic features of ultrafast transient-absorption signals related to the probed-frequency dependence of vibrational quantum beats. These include a Stokes-shifting node at the time-evolving peak emission frequency, antiphasing between vibrational oscillations on opposite sides (i.e., to the red or blue) of this node, and spectral fingering due to vibrational overtones and combinations. Our calculations make a vibrationally abrupt approximation for the incident pump and probe pulses, but properly account for temporal pulse overlap and signal turn-on, rather than neglecting pulse overlap or assuming delta-function excitations, as are sometimes done.

Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I ß-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the ß-turn not otherwise involved in a hydrogen bond. This ß-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y ß-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

Two-Dimensional Visible Spectroscopy For Studying Colloidal Semiconductor Nanocrystals.

Possibilities offered by 2D visible spectroscopy for the investigation of the properties of excitons in colloidal semiconductor nanocrystals are overviewed, with a particular focus on their ultrafast dynamics. The technique of 2D electronic spectroscopy is illustrated with several examples showing its advantages compared to 1D ultrafast spectroscopic techniques (transient absorption and time-resolved photoluminescence).

Methylene Blue Exciton States Steer Nonradiative Relaxation: Ultrafast Spectroscopy of Methylene Blue Dimer.

The photochemistry and aggregation properties of methylene blue (MB) lead to its popular use in photodynamic therapy. The facile formation of strongly coupled "face-to-face" H-aggregates in concentrated aqueous solution, however, significantly changes its spectroscopic properties and photophysics. The photoinitiated dynamics of the simplest MB aggregate, MB2, was investigated over femtosecond to nanosecond time scales revealing sequential internal conversion events that fully relax the excited population. MB monomer dynamics were analyzed in tandem for a direct comparison. First, ultrafast internal conversion from the electric-dipole allowed upper exciton state to the lower forbidden exciton state was evaluated by use of broadband transient absorption (BBTA) and two-dimensional electronic spectroscopy (2DES) with a time resolution of ∼ 10 fs. Lineshape analysis of MB and MB2 2DES bands at 298 and 77 K show effectively no difference in the diagonal/antidiagonal line width ratio for the dimer, in marked contrast to the distinct reduction of the homogeneous line width for MB. This result is interpreted as ultrafast population relaxation imposing a limitation to the homogeneous line width, instead of pure dephasing as in the case of the monomer. Narrowband transient absorption was performed with the aid of target analysis, to model the dynamics at longer times. The MB dynamics were described by a sequential model featuring vibrational relaxation (1-10 ps) followed by intersystem crossing and internal conversion (τ ∼ 370 ps) leaving behind MB triplet species. Alternatively, the dimer dynamics were entirely quenched within ∼ 10 ps, yielding a ground state recovery time of 3-4 ps. Such fast and complete relaxation to the ground state demonstrates the effect of concentration quenching when monomers are brought into close proximity. The formation of exciton states introduces an initial energy funnel that eventually leads to population relaxation to the ground state, preventing even the dissociation of dimers despite having internal energies well above its binding energy.

Observing Vibrational Wavepackets during an Ultrafast Electron Transfer Reaction.

Recent work has proposed that coherent effects impact ultrafast electron transfer reactions. Here we report studies using broadband pump-probe and two-dimensional electronic spectroscopy of intramolecular nuclear motion on the time scale of the electron transfer between oxazine 1 (Ox1) and dimethylaniline (DMA). We performed time-frequency analysis on the time domain data to assign signal amplitude modulations to ground or excited electronic states in the reactive system (Ox1 in DMA) relative to the control system (Ox1 in chloronaphthalene). It was found that our ability to detect vibrational coherence via the excited electronic state of Ox1 diminishes on the time scale that population is lost by electron transfer. However, the vibrational wavepacket is not damped by the electron transfer process and has been observed previously by detecting the Ox1 radical transient absorption. The analysis presented here indicates that the "addition" of an electron to the photoexcited electron acceptor does not significantly perturb the vibrational coherence, suggesting its presence as a spectator, consistent with the Born-Oppenheimer separation of electronic and nuclear degrees of freedom.

Broadband Transient Absorption and Two-Dimensional Electronic Spectroscopy of Methylene Blue.

Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of methylene blue in aqueous solution are reported. By isolating the coherent oscillations of the nonlinear signal amplitude and Fourier transforming with respect to the population time, we analyzed a significant number of coherences in the frequency domain and compared them with predictions of the vibronic spectrum from density function theory (DFT) calculations. We show here that such a comparison enables reliable assignments of vibrational coherences to particular vibrational modes, with their constituent combination bands and overtones also being identified via Franck­Condon analysis aided by DFT. Evaluation of the Fourier transform (FT) spectrum of transient absorption recorded to picosecond population times, in coincidence with 2D oscillation maps that disperse the FT spectrum into the additional excitation axis, is shown to be a complementary approach toward detailed coherence determination. Using the Franck­Condon overlap integrals determined from DFT calculations, we modeled 2D oscillation maps up to two vibrational quanta in the ground and excited state (six-level model), showing agreement with experiment. This semiquantitative analysis is used to interpret the geometry change upon photoexcitation as an expansion of the central sulfur/nitrogen containing ring due to the increased antibonding character in the excited state.

UV photofragmentation and IR spectroscopy of cold, G-type ß-O-4 and ß-ß dilignol-alkali metal complexes: structure and linkage-dependent photofragmentation.

Ultraviolet photofragmentation spectroscopy and infrared spectroscopy were performed on two prototypical guaiacyl (G)-type dilignols containing ß-O-4 and ß-ß linkages, complexed with either lithium or sodium cations. The complexes were generated by nanoelectrospray ionization, introduced into a multistage mass spectrometer, and subsequently cooled in a 22-pole cold ion trap to T ≈ 10 K. A combination of UV photofragment spectroscopy and IR-UV double resonance spectroscopy was used to characterize the preferred mode of binding of the alkali metal cations and the structural changes so induced. Based on a combination of spectral evidence provided by the UV and IR spectra, the Li(+) and Na(+) cations are deduced to preferably bind to both dilignols via their linkages, which constitute unique, oxygen-rich binding pockets for the cations. The UV spectra reflect this binding motif in their extensive Franck-Condon activity involving low-frequency puckering motions of the linkages in response to electronic excitation. In the pinoresinol•Li(+)/Na(+) complexes involving the ß-ß linkage, the spectra also showed an inherent spectral broadening. The photofragment mass spectra are unique for each dilignol•Li(+)/Na(+) complex, many of which are also complementary to those produced by collision-induced dissociation (CID), indicating the presence of unique excited state processes that direct the fragmentation. These results suggest the potential for site-selective fragmentation and for uncovering fragmentation pathways only accessed by resonant UV excitation of cold lignin ions.

Fermi resonance effects in the vibrational spectroscopy of methyl and methoxy groups.

A theoretical model Hamiltonian [J. Chem. Phys. 2013, 138, 064308] for describing vibrational spectra associated with the CH stretch of CH2 groups is extended to molecules containing methyl and methoxy groups. Results are compared to the infrared (IR) spectroscopy of four molecules studied under supersonic expansion cooling in gas phase conditions. The molecules include 1,1-diphenylethane (DPE), 1,1-diphenylpropane (DPP), 2-methoxyphenol (guaiacol), and 1,3-dimethoxy-2-hydroxybenzene (syringol). Transforming the bending normal mode vibrations of CH3 groups to local scissor vibrations leads to model Hamiltonians which share many features present in our model Hamiltonian for the stretching vibrations of CH2 Fermi coupled to scissor modes. The central difference arises from the greater scissor-scissor coupling present in the CH3 case. Comparing anharmonic couplings between these modes and the stretch-bend Fermi coupling for a variety of systems, it is observed that the anharmonic couplings are robust; their values are similar for the four molecules studied as well as for ethane and methanol. Similar results are obtained with both density functional theory and coupled-cluster calculations. This robustness suggests a new parametrization of the model Hamiltonian that reduces the number of fitting parameters. In contrast, the harmonic contributions to the Hamiltonian vary substantially between the molecules leading to important changes in the spectra. The resulting Hamiltonian predicts most of the major spectral features considered in this study and provides insights into mode mixing and the consequences of the mixing on dynamical processes that follow ultrafast CH stretch excitation.