Activity

It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed a wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin, which adopts the most populated ternary structures determined from the molecular dynamics simulations, followed by ab initio quantum mechanical (QM) calculations on all 12 amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential in the context of a classical or polarizable force field (PFF). We discovered that the atomic radius of Ca2+ in conventional force fields is too large for the QM calculation to capture the variation in the coordination geometry of Ca2+ in its ionic form, leading to unphysical charges. Specifically, we found that the fitted atomic charges of Ca2+ in the context of PFF depend on the coordinating geometry of electronegative atoms from the amino acids in the loop. Although nearby water molecules do not influence the atomic charge of Ca2+, they are crucial for compensating for the coordination of Ca2+ due to the conformational flexibility in the EF-hand loop. Our method advances the development of force fields for metal ions and protein binding sites in dynamic environments.Mechanical spectral hole burning (MSHB) has been used to investigate the nonlinear dynamics in polymers, ranging from melts, solutions, block co-polymers, and glasses. MSHB was developed as an analog to the dielectric spectral hole burning method, which is not readily applicable in polymers due to weak dielectric response. While similar holes were observed in both mechanical and dielectric hole burning, the interpretations were different. In the latter case, it has been argued that the holes are related to dynamic heterogeneity as related to an increase in the local temperature of molecular sub-ensembles (spatial heterogeneity), while in the former case, the holes have been related to the type of dynamics (rubbery, Rouse, etc.). Recent work from our laboratories used MSHB to investigate glassy poly(methyl methacrylate) and showed evidence of hole burning and supported the hypothesis that the origin of holes was related to dynamic heterogeneity as evidenced by the holes being developed near the strong β-relaxation in PMMA. In this work, MSHB is used to study polycarbonate, which has a weak β-relaxation, and the results are compared with those observed in PMMA. We observe that the polycarbonate exhibits weak holes and the nature of the holes with a change in pump amplitude and frequency is different than observed in PMMA. These results support the hypothesis that the hole burning observed in amorphous polymers below the glass transition temperature is related to the strength of the β-transition, which, in turn, is related to molecular level heterogeneity in the material dynamics.We present the non-adiabatic Matsubara dynamics, a general framework for computing the time-correlation function (TCF) of electronically non-adiabatic systems. This new formalism is derived based on the generalized Kubo-transformed TCF using the Wigner representation for both the nuclear degrees of freedom and the electronic mapping variables. By dropping the non-Matsubara nuclear normal modes in the quantum Liouvillian and explicitly integrating these modes out from the expression of the TCF, we derived the non-adiabatic Matsubara dynamics approach. Further making the approximation to drop the imaginary part of the Matsubara Liouvillian and enforce the nuclear momentum integral to be real, we arrived at the non-adiabatic ring-polymer molecular dynamics (NRPMD) approach. We have further justified the capability of NRPMD for simulating the non-equilibrium TCF. This work provides the rigorous theoretical foundation for several recently proposed state-dependent RPMD approaches and offers a general framework for developing new non-adiabatic quantum dynamics methods in the future.We report on systematic changes to the adsorption geometry of the dye N3 [cis-bis(isothiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato ruthenium(II)] on a gold substrate as the pH of the deposition environment is altered. The protonation states of the four -COOH groups of the N3 dye change according to the modified pH conditions, thus affecting the number of -COOH and -NCS functional groups that participate in the adsorption to gold. Here, we use heterodyne detected vibrational sum frequency generation (HD-VSFG) spectroscopy to obtain surface specific vibrational information on both -COOH and -NCS groups as a function of pH of the deposition conditions. Polarization-dependent HD-VSFG yields sets of complex χ(2) spectra, enabling us to perform a simultaneous fitting procedure to the polarization-dependent real and imaginary components and thus extract detailed structural information of the N3/gold interface. Our results show that N3 preferentially adsorbs to gold either with two -COOH groups and one -NCS group in more acidic conditions or with one -COOH group and two -NCS groups in more basic conditions.Electronic structure methods emerging from the combination of multiconfigurational wave functions and density functional theory (DFT) aim to take advantage of the strengths of the two nearly antagonistic theories. One of the common strategies employed to merge wave function theory (WFT) with DFT relies on the range separation of the Coulomb operator in which DFT functionals take care of the short-distance part, while long-range inter-electronic interactions are evaluated by using the chosen wave function method (WFT-srDFT). In this work, we uncover the limitations of WFT-srDFT in the characterization of open-shell systems. SBEβCD We show that spin polarization effects have a major impact on the (short-range) DFT exchange energy and are of vital importance in order to provide a balanced description between closed and open-shell configurations. We introduce different strategies to account for spin polarization in the short range based on the definition of a spin polarized electron density and with the use of short-range exact exchange.