Two-dimensional ultraviolet spectroscopy of proteins

Two-dimensional ultraviolet (2DUV) spectroscopy is a novel technology for probing molecular structure. We have developed a generalized quantum mechanics/molecular mechanics (QM/MM) approach to simulate the electronic transitions of protein backbones and aromatic amino acids in aqueous solution. These transitions, which occur in the ultraviolet (UV) region, provide a sensitive probe of molecular structure. The features of 2DUV spectra are accurately characterized and enable us to trace small variations in the structure and dynamics as well as evolution propensity with high accuracy. Various structures and dynamic phenomena are investigated to construct a systematic framework for 2DUV simulation mechanisms, so as to explore further applications of this technique. In this feature article, we summarize the theory and applications of 2DUV spectroscopy we have engaged in recently, present the important roles of 2DUV spectroscopy, and outline directions for future development. We hope this article can offer a platform for more scientists in different research fields to gain a clear overview of 2DUVand further attract more people to explore this promising field.     

Dye Probes of Nanoclusters in Liquids

Calculations have been carried out to optimize the structure of Van der Waals complexes of methanol with N-methyl-2-nitroaniline, a dye capable of shifts in visible and ultraviolet spectra that depend on (1) solvent dielectric, (2) solvent shell structure, and (3) hydrogen bonding to a slight extent. Hartree–Fock–Roothaan calculations with various basis sets and single-excitation configuration interaction (SCI) are compared to Density–Functional–Theory Time-Dependent Hartree–Fock (DFT-TD) results for three low-energy ultraviolet electronic transitions. Energy-minimized structures are reported for a trimeric complex of two methanol-one water as found using a 6-311G** basis indicating two possible hydrogen-bonding schemes. The effect of a dielectric medium on the ultraviolet spectrum is compared to gas-phase clusters. Electronic transitions are also given for the dye-probe complexed with four or five methanol molecules finding good agreement with observed shifts in the ultraviolet spectrum as found with the TDHF-DFT formalism for the lowest energy transition near 425nm.     

Exploring the ability of frozen-density embedding to model induced circular dichroism

In this study, we present calculations of the circular dichroism (CD) spectra of complexes between achiral and chiral molecules. Nonzero rotational strengths for transitions of the nonchiral molecule are induced by interactions between the two molecules, which cause electronic and/or structural perturbations of the achiral molecule. We investigate if the chiral molecule (environment) can be represented only in terms of its frozen electron density, which is used to generate an effective embedding potential. The accuracy of these calculations is assessed in comparison to full supermolecular calculations. We can show that electronic effects arising from specific interactions between the two subsystems can reliably be modeled by the frozen-density representation of the chiral molecule. This is demonstrated for complexes of 2-benzoylbenzoic acid with (-)-(R)-amphetamine and for a nonchiral, artificial amino acid receptor system consisting of ferrocenecarboxylic acid bound to a crown ether, for which a complex with l-leucine is studied. Especially in the latter case, where multiple binding sites and interactions between receptor and target molecule exist, the frozen-density results compare very well with the full supermolecular calculation. We also study systems in which a cyclodextrin cavity serves as a chiral host system for a small, achiral molecule. Problems arise in that case because of the importance of excitonic couplings with excitations in the host system. The frozen-density embedding cannot describe such couplings but can only capture the direct effect of the host electron density on the electronic structure of the guest. If couplings play a role, frozen-density embedding can at best only partially describe the induced circular dichroism. To illustrate this problem, we finally construct a case in which excitonic coupling effects are much stronger than direct interactions of the subsystem densities. The frozen density embedding is then completely unsuitable.     

Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

The unusual electronic properties of directly linked 1,4-polyanthraquinones (14PAQs) are investigated. The dihedral angle between the molecular planes of anthraquinones (AQs) is found to be close to 90°. Contrary to the prevailing notion that the interaction between orthogonal units is negligible due to broken π-electron conjugation, the coupling between neighboring AQ units does not have a minimum at 90° and is much larger than that expected. The unexpectedly large electronic coupling between orthogonal AQ units is explained by the interaction between the lone pairs of the carbonyl oxygen and the π system of the neighboring unit, which allows favorable overlap between frontier molecular orbitals at the orthogonal geometry. It is shown that this effect, which is described computationally for the first time, can be strengthened by adding more quinone units. The effect of thermal fluctuations on the couplings is assessed through ab initio molecular dynamics simulations. The distributions of the couplings reveal that electron transport is resilient to dynamic disorder in all systems considered, whereas the hole couplings are much more sensitive to disorder. Lone pair–π interactions are described, as a previously largely overlooked conjugation mechanism, for incorporation into a new class of disorder-resilient semiconducting redox polymers.     

Multiple solvation configurations around phthalocyanine in helium droplets

Recent measurements of the emission spectrum of phthalocyanine solvated in superfluid helium nanodroplets exhibit a constant 10.3 cm(-1) splitting of each emission line relative to the absorption spectrum. This splitting has been attributed to two distinct helium environments near the surface of the phthalocyanine molecule. Rigid-body path-integral Monte Carlo provides a means of investigating the origin of the splitting on a detailed microscopic level. Path-integral Monte Carlo simulations of 4He(N)-phthalocyanine at 0.625 K with N ranging from 24 to 150 show two distinct helium configurations. One configuration is commensurate with the molecular substrate and the other is a triangular lattice. We investigate the energetics of these two configurations and use a method for calculating electronic spectral shifts for aromatic molecule-rare-gas clusters due to dispersive interactions to estimate the spectral splitting that would arise from the two helium configurations seen for N=150. The results are in reasonable agreement with the experimentally measured splitting, supporting the existence of two distinct local helium environments near the surface of the molecule in the nanodroplets.     

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.     

Tunneling currents that increase with molecular elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.     

Coriolis coupling effects on the initial-state-resolved dynamics of the N(2D)+H2-->NH+H reaction

We present Coriolis coupling effects on the initial-state-resolved dynamics of the insertion reaction N((2)D)+H(2)(X (1)Sigma(g) (+))-->NH(X (3)Sigma(-) and a (1)Delta)+H((2)S), without and with nonadiabatic Renner-Teller (RT) interactions between the NH(2) X (2)B(1) and A (2)A(1) electronic states. We report coupled-channel (CC) Hamiltonian matrix elements, which take into account both Coriolis and RT couplings, use the real wave-packet and flux methods for calculating initial-state-resolved reaction probabilities, and contrast CC with centrifugal-sudden (CS) results. Without RT interactions, Coriolis effects are rather small up to J=40, and the CS approximation can be safely employed for calculating initial-state-resolved, integral cross sections. On the other hand, RT effects are associated with rather large Coriolis couplings, mainly near the linearity of NH(2), and the accuracy of the CS approximation thus breaks down at high collision energies, when the reaction starts on the excited A (2)A(1) surface. We also present the CC-RT distribution of the X (3)Sigma(-) and a (1)Delta electronic states of the NH products.     

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces

Accurate infrared spectra of the two hydroxycarbene isomers are computed by diagonalizing the Watson Hamiltonian including up to four mode couplings using full dimensional potential energy and dipole moment surfaces calculated at the CCSD(T)/cc-pVTZ (frozen core) and CCSD6-311G(**) (all electrons correlated) levels, respectively. Anharmonic corrections are found to be very important for these elusive higher-energy isomers of formaldehyde. Both the energy levels and intensities of stretching fundamentals and all overtone transitions are strongly affected by anharmonic couplings between the modes. The results for trans-HCOHHCOD are in excellent agreement with the recently reported IR spectra, which validates our predictions for the cis-isomers.     

First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide

By combining time-dependent density functional theory (TDDFT) and molecular dynamics (MD) simulations, we calculate the ultraviolet absorption and circular dichroism (CD) of a cyclic dipeptide, cyclo(L-Pro-D-Tyr), in the 185-300 nm region. The absorption is dominated by the phenol chromophore of tyrosine. The CD spectrum shows both phenol and amide units transitions. A crude coherent two-dimensional ultraviolet spectrum (2DUV) calculated by neglecting the two-excitation states shows a cross-peak between two transitions of the phenol in the tyrosine side chain. Additional cross-peaks between the side chain and the backbone are observed when using a chirality-induced pulse polarization configuration.     

Ultrafast Structural Dynamics of Biomolecules Examined by Multiple‐Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L ‐α‐glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal‐mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two‐dimensional infrared (2D IR) spectra, which are simulated using time‐domain third‐order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.     

The Impact of Interlayer Electronic Coupling on Charge Transport in Organic Semiconductors: A Case Study on Titanylphthalocyanine Single Crystals

Traditionally, it is believed that three‐dimensional transport networks are preferable to those of lower dimensions. We demonstrate that inter‐layer electronic couplings may result in a drastic decrease of charge mobilities by utilizing field‐effect transistors (FET) based on two phases of titanyl phthalocyanine (TiOPc) crystals. The α‐phase crystals with electronic couplings along two dimensions show a maximum mobility up to 26.8 cm² V^?1 s^?1. In sharp contrast, the β‐phase crystals with extra significant inter‐layer electronic couplings show a maximum mobility of only 0.1 cm² V^?1 s^?1. Theoretical calculations on the bulk crystals and model slabs reveal that the inter‐layer electronic couplings for the β‐phase devices will diminish remarkably the device charge transport abilities owing to the coupling direction perpendicular to the current direction. This work provides new insights into the impact of the dimensionality and directionality of the packing arrangements on charge transport in organic semiconductors.     

Spectroscopy of the cyano radical in an aqueous environment

The effect of bulk water on the B (2)Sigma(+) <-- X (2)Sigma(+) and A (2)Pi <-- X (2)Sigma(+) electronic transitions of the cyano radical is investigated. First, the cyano radical-water dimer is characterized to understand the nature of the interactions and parametrize molecular mechanics (MM) potentials. The carbon atom, which hosts the unpaired electron, is found to have a Lennard-Jones radius smaller than typical force fields values. Classical molecular dynamics (MD) is then used to sample water configurations around the radical, employing two sets of MM parameters for the cyano radical and water. Subsequently, vertical excitation energies are calculated using time-dependent density functional theory (TD-DFT) and equation-of-motion coupled-cluster with single and double substitutions (EOM-CCSD). The effect of water is modeled by point charges used in the MD simulations. It is found that both bands blue-shift with respect to their gas phase position; the magnitude of the shift is only weakly dependent on the method and the MM parameter set used. The calculated shifts are analyzed in terms of the solute-solvent interactions in the ground and excited states. Significant contributions come from valence repulsion and electrostatics. Consequences for experiments on ICN photodissociation in water are discussed.     

Nonadiabatic transitions in chemical reactions: A quantum mechanical study

This work presents an exact quantum mechanical treatment of a reactive three-atom collinear model system incorporating nonadiabatic couplings. It was assumed that nonadiabatic transitions are induced by the vibrational motion only. The main findings are: (i) The reaction process can create conditions in which weak nonadiabatic couplings terms ( for which the Massey parameter was round 10) may cause large probabilities (～0.5) for transitions from one electronic surface to the other. In other words, the reaction process is able in certain cases to create a near resonance situation which makes the non-adiabatic transition almost independent of the magnitude of the coupling term. For this to happen the two surfaces need not be proximate, nor need they “almost” cross along a certain line (ii) In cases where the main nonadiabatic transitions take place outside the interaction region one may, at least qualitatively, decouple the reaction process from the nonadiabatic one. Thus, under the conditions specified one may first treat the reactive system on the ground state surface without including the excited interacting surface and then treat the nonadiabatic process independently.     

Dications of bis-triarylamino-[2.2]paracyclophanes: Evaluation of excited state couplings by GMH analysis

In this paper, we present the absorption properties of a series of bis-triarylamino-[2.2]paracyclophane diradical dications. The localized pi-pi and the charge-transfer (CT) transitions of these dications are explained and analyzed by an exciton coupling model that also considers the photophysical properties of the "monomeric" triarylamine radical cations. Together with AM1-CISD-calculated transition moments, experimental transition moments and transition energies of the bis-triarylamine dications were used to calculate electronic couplings by a generalized Mulliken-Hush (GMH) approach. These couplings are a measure for interactions of the excited mixed-valence CT states. The modification of the diabatic states reveals similarities of the GMH three-level model and the exciton coupling model. Comparison of the two models shows that the transition moment between the excited mixed-valence states mu(ab) of the dimer equals the dipole moment difference Delta of the ground and the excited bridge state of the corresponding monomer.     

Visualizations of transition dipoles, charge transfer, and electron-hole coherence on electronic state transitions between excited states for two-photon absorption

The one-photon absorption (OPA) properties of donor-pi-bridge-acceptor-pi-bridge-donor (D-pi-A-pi-D)-type 2,1,3-benzothiadiazoles (BTD) were studied with two dimensional (2D) site and three dimensional (3D) cube representations. The 2D site representation reveals the electron-hole coherence on electronic state transitions from the ground state. The 3D representation shows the orientation of transition dipole moment with transition density, and the charge redistribution on the excited states with charge difference density. In this paper, we further developed the 2D site and 3D cube representations to investigate the two-photon absorption (TPA) properties of D-pi-A-pi-D-type BTD on electronic transitions between excited states. With the new developed 2D site and 3D cube representations, the orientation of transition dipole moment, the charge redistribution, and the electron-hole coherence for TPA of D-pi-A-pi-D-type BTD on electronic state transitions between excited states were visualized, which promote deeper understanding to the optical and electronic properties for OPA and TPA.     

Electronic transitions and vibronic coupling in neptunyl compounds

The low-lying electronic transitions of the neptunyl (NpO(2)(2+)) ion are characterized as either charge transfer (CT) or intra- 5f. Comparison of these classes of electronic transitions reveals significantly different photophysical properties, especially in vibronic coupling. An empirical model developed for analyses of uranyl CT vibronic transitions is used here to simulate the absorption (excitation) spectra of neptunyl in two compounds of different chemical compositions and structural symmetries. Analyses reveal that CT vibronic coupling in neptunyl has the same characteristics as that in typical uranyl analogues. The primary profile of the CT spectra is similar for neptunyl respectively with respect to chloride- and oxide-neptunium bonding interactions. On the other hand, vibronic coupling to the CT transitions is significantly different from that of f-f transitions, even within a given neptunyl compound. Electronic energy levels, vibronic coupling strength, and frequencies of various vibration modes were evaluated for transitions to the excited states of different origins in the region from 8000 cm(-1) to 21000 cm(-1) for two neptunyl compounds.     

Chasing charge localization and chemical reactivity following photoionization in liquid water

The ultrafast dynamics of the cationic hole formed in bulk liquid water following ionization is investigated by ab initio molecular dynamics simulations and an experimentally accessible signature is suggested that might be tracked by femtosecond pump-probe spectroscopy. This is one of the fastest fundamental processes occurring in radiation-induced chemistry in aqueous systems and biological tissue. However, unlike the excess electron formed in the same process, the nature and time evolution of the cationic hole has been hitherto little studied. Simulations show that an initially partially delocalized cationic hole localizes within ~30 fs after which proton transfer to a neighboring water molecule proceeds practically immediately, leading to the formation of the OH radical and the hydronium cation in a reaction which can be formally written as H(2)O(+) + H(2)O → OH + H(3)O(+). The exact amount of initial spin delocalization is, however, somewhat method dependent, being realistically described by approximate density functional theory methods corrected for the self-interaction error. Localization, and then the evolving separation of spin and charge, changes the electronic structure of the radical center. This is manifested in the spectrum of electronic excitations which is calculated for the ensemble of ab initio molecular dynamics trajectories using a quantum mechanics/molecular mechanics (QM∕MM) formalism applying the equation of motion coupled-clusters method to the radical core. A clear spectroscopic signature is predicted by the theoretical model: as the hole transforms into a hydroxyl radical, a transient electronic absorption in the visible shifts to the blue, growing toward the near ultraviolet. Experimental evidence for this primary radiation-induced process is sought using femtosecond photoionization of liquid water excited with two photons at 11 eV. Transient absorption measurements carried out with ~40 fs time resolution and broadband spectral probing across the near-UV and visible are presented and direct comparisons with the theoretical simulations are made. Within the sensitivity and time resolution of the current measurement, a matching spectral signature is not detected. This result is used to place an upper limit on the absorption strength and/or lifetime of the localized H(2)O(+) ((aq)) species.     

The role of the Mg2+ cation in ATPsynthase studied by electron paramagnetic resonance using VO2+ and Mn2+ paramagnetic probes

The electron paramagnetic resonance (EPR), electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) spectra of Mg2+-depleted chloroplast F1-ATPase substituted with stoichiometric VO2+ are reported. The ESEEM and HYSCORE spectra of the complex are dominated by the hyperfine and quadrupole interactions between the VO2+ paramagnet and two different nitrogen ligands with isotropic hyperfine couplings /A1/ = 4.11 MHz and /A2/ = 6.46 MHz and nuclear quadrupole couplings e2qQ1 approximately 3.89-4.49 MHz and e2qQ2 approximately 1.91-2.20 MHz, respectively. Aminoacid functional groups compatible with these magnetic couplings include a histidine imidazole, the epsilon-NH2 of a lysine residue, and the guanidinium group of an arginine. Consistent with this interpretation, very characteristic correlations are detected in the HYSCORE spectra between the 14N deltaM1 = 2 transitions in the negative quadrant, and also between some of the deltaM1 = 1 transitions in the positive quadrant. The interaction of the substrate and product ADP and ATP nucleotides with the enzyme has been studied in protein complexes where Mg2+ is substituted for Mn2+. Stoichiometric complexes of Mn x ADP and Mn x ATP with the whole enzyme show distinct and specific hyperfine couplings with the 31P atoms of the bonding phosphates in the HYSCORE (ADP, A(31Pbeta) = 5.20 MHz: ATP, A(31Pbeta) = 4.60 MHz and A(31Pgamma) = 5.90 MHz) demonstrating the role of the enzyme active site in positioning the di- or triphosphate chain of the nucleotide for efficient catalysis. When the complexes are formed with the isolated alpha or beta subunits of the enzyme, the HYSCORE spectra are substantially modified, suggesting that in these cases the nucleotide binding site is only partially structured.