Antibody recognition of chiral surfaces. Enantiomorphous crystals of leucine-leucine-tyrosine

Monoclonal antibodies were selected after immunization with crystals of the tripeptide l-leucine-l-leucine-l-tyrosine. They interact with the tripeptide crystals, but do not interact with the tripeptide molecule, with other crystalline surfaces, or with adsorbed protein. The interactions of two antibodies with crystals of l-Leu-l-Leu-l-Tyr and of its enantiomer d-Leu-d-Leu-d-Tyr were characterized in depth. Antibody 48E is stereoselective and enantioselective: it recognizes only the [011] faces of the l-Leu-l-Leu-l-Tyr crystals, and not the enantiomorphous [011] faces of d-Leu-d-Leu-d-Tyr crystals, or any other faces of either crystal. In contrast, antibody 602E is poorly stereoselective and is not enantioselective: it recognizes the crystals of both enantiomers, interacting with a number of different faces of each. The different recognition patterns are explained on the basis of the nature of the interactions and the structure of the interacting surfaces. Understanding this antibody specificity advances our general understanding of surface recognition and transfer of chiral information across biological interfaces.     

A comparison between different semiclassical approximations for optical response functions in nonpolar liquid solutions

The temporal behavior of optical response functions (ORFs) reflects the quantum dynamics of an electronic superposition state, and as such lacks a well-defined classical limit. In this paper, we consider the importance of accounting for the quantum nature of the dynamics when calculating ORFs of different types. To this end, we calculated the ORFs associated with the linear absorption spectrum and the nonlinear two-pulse photon-echo experiment, via the following approaches: (1) the semiclassical forward-backward approach; (2) an approach based on linearizing the path-integral forward-backward action in terms of the difference between the forward and backward paths; (3) an approach based on ground state nuclear dynamics. The calculations were performed on a model that consists of a two-state chromophore solvated in a nonpolar liquid. The different methods were found to yield very similar results for the absorption spectrum and "diagonal" two-pulse photon echo (i.e., the homodyne-detected signal at time t=t(0) after the second pulse, where t(0) is the time interval between the two pulses). The different approximations yielded somewhat different results in the case of the time-integrated photon-echo signal. The reasons for the similarity between the predictions of different approximations are also discussed.     

Vibrational energy relaxation rates via the linearized semiclassical approximation: applications to neat diatomic liquids and atomic-diatomic liquid mixtures

We report the results obtained from the application of our previously proposed linearized semiclassical method for computing vibrational energy relaxation (VER) rates (J. Phys. Chem. A 2003, 107, 9059, 9070) to neat liquid oxygen, neat liquid nitrogen, and liquid mixtures of oxygen and argon. Our calculations are based on a semiclassical approximation for the quantum-mechanical force-force correlation function, which puts it in terms of the Wigner transforms of the force and the product of the Boltzmann operator and the force. The calculation of the multidimensional Wigner integrals is made feasible by the introduction of a local harmonic approximation. A systematic analysis has been performed of the temperature and mole-fraction dependences of the VER rate constant, as well as the relative contributions of centrifugal and potential forces, and of different types of quantum effects. The results were found to be in very good quantitative agreement with experiment, and they suggest that this semiclassical approximation can capture the quantum enhancement, by many orders of magnitude, of the experimentally observed VER rate constants over the corresponding classical predictions.     

A computational study of the correlations between structure and dynamics in free and surface-immobilized single polymer chains

The correlations between structure and dynamics in free and surface-immobilized polymers were investigated via Langevin dynamics simulations of a free-jointed homopolymer. A detailed analysis was performed for a polymer in free solution and a polymer attached to a surface. The cases of repulsive and attractive surfaces, as well as poor and good solvents, were considered. The analysis focuses on properties that are particularly relevant to single molecule measurements, namely: (1) the distribution of end-to-end distance, (2) the correlations between the conformational structure and the time scale of its motion, (3) the correlations, at equilibrium, between the end-to-end distance and its displacement, and (4) the correlation between the initial coil conformation and the collapse pathway into the globular state. The differences and similarities between this model and a previously considered model of a protein, with two-state folding kinetics and a well-defined native state, are also discussed.     

Homogeneity and Markovity of electronic dephasing in liquid solutions

The electronic dephasing dynamics of a solvated chromophore is formulated in terms of a non-Markovian master equation. Within this formulation, one describes the effect of the nuclear degrees of freedom on the electronic degrees of freedom in terms of a memory kernel function, which is explicitly dependent on the initial solvent configuration. In the case of homogeneous dynamics, this memory kernel becomes independent of the initial configuration. The Markovity of the dephasing process is also the most conveniently explored by comparing the results obtained via the non-Markovian master equation to these obtained via its Markovian counterpart. The homogeneous memory kernel is calculated for a two-state chromophore in liquid solution, and used to explore the sensitivity of photon echo signals to the heterogeneity and non-Markovity of the underlying solvation dynamics.     

Classical vs quantum vibrational energy relaxation pathways in solvated polyatomic molecules

Vibrational energy relaxation (VER) of solvated polyatomic molecules can occur via different pathways. In this paper, we address the question of whether treating VER classically or quantum-mechanically can lead to different predictions with regard to the preferred pathway. To this end, we consider the relaxation of the singly excited asymmetric stretch of a rigid, symmetrical, and linear triatomic molecule (A-B-A) in a monatomic liquid. In this case, VER can occur either directly to the ground state or indirectly via intramolecular vibrational relaxation (IVR) to the symmetric stretch. We have calculated the rates of these two different VER pathways via classical mechanics and the linearized semiclassical (LSC) method. When the mass of the terminal A atoms is significantly larger than that of the central B atom, we find that LSC points to intermolecular VER as the preferred pathway, whereas the classical treatment points to IVR. The origin of this trend reversal appears to be purely quantum-mechanical and can be traced back to the significantly weaker quantum enhancement of solvent-assisted IVR in comparison to that of intermolecular VER.     

Ab initio calculation of the electronic absorption of functionalized octahedral silsesquioxanes via time-dependent density functional theory with range-separated hybrid functionals

Recent advances in the ability to functionalize octahedral silsesquioxanes with different photoactive ligands, and thereby tune their optical properties, suggest that these molecules may serve as potential building blocks of light-harvesting, photovoltaic, and photonic devices. In this paper we report extensive ab initio calculations of the excitation energies underlying the absorption spectra of these systems. The calculations are based on density functional theory for the ground electronic state and time-dependent density functional theory for the excited electronic states. The ability of the commonly used B3LYP functional to reproduce the experimentally observed absorption excitation energies is compared to that of recently developed range-separated hybrid functionals. The importance of pairing the range-separated hybrid functionals with basis sets that include diffuse and polarization basis functions is demonstrated in the case of vinyl-functionalized silsesquioxanes. Absorptive excitation energies are then calculated and compared with experiment for octahedral silsesquioxanes functionalized with larger ligands. The tunability of optical properties is demonstrated by considering the effect on the excitation energies of functionalizing the ligands with electron-donating or -withdrawing groups.     

A nonperturbative calculation of nonlinear spectroscopic signals in liquid solution

Nonlinear spectroscopic signals in liquid solution were calculated without treating the field-matter interaction in a perturbative manner. The calculation is based on the assumption that the intermolecular degrees of freedom can be treated classically, while the time evolution of the electronic state is treated quantum mechanically. The calculated overall electronic polarization is then resolved into its directional components via the method of Seidner et al. [J. Chem. Phys. 103, 3998 (1995)]. It is shown that the time dependence of the directional components is independent of laser intensity in the impulsive pulse regime, which allows for flexibility in choosing the procedure for calculating optical response functions. The utility and robustness of the nonperturbative procedure is demonstrated in the case of a two-state chromophore solvated in a monoatomic liquid, by calculating nonlinear time-domain signals in the strong-field, weak-field, impulsive, and nonimpulsive regimes.     

Protein structure and dynamics from single-molecule fluorescence resonance energy transfer

The pros and cons of single-molecule vs ensemble-averaged fluorescence resonance energy transfer (FRET) experiments, performed on proteins, are explored with the help of Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined native state and two-state folding kinetics. A detailed analysis of the distribution of the donor-acceptor distance is presented at different points along the denaturation curve, along with its dependence on the averaging time window. We show that unique information on the correlation between structure and dynamics, which can only be obtained from single-molecule experiments, is contained in the correlation between the donor-acceptor distance and its displacement. The latter is shown to provide useful information on the free energy landscape of the protein, which is complementary to that obtained from the distribution of donor-acceptor distances.