Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach

Systematic probing of local environments around biopolymers is important for understanding their functions. Therefore, there has been growing interest in in situ measurements of molecular granularity and heterogeneity through the systematic analysis of vibrational frequency shifts of carbonyl and nitrile infrared probes by vibrational Stark dipole theory. However, here we show that the nitrile vibrational frequency shift induced by its interaction with the surrounding molecules cannot be solely described by electric field-based theory because of the exchange-repulsion and dispersion interaction contributions. Considering a variety of molecular environments ranging from bulk solutions to protein environments, we explore the distinct scenarios of solute-environment contacts and their traces in vibrational frequency shifts. We believe that the present work could provide a set of clues that could be potentially used to design a rigorous theoretical model linking vibrational solvatochromism and molecular topology in complex heterogeneous environments. ©the Owner Societies 2016123261sciescopu

Ab Initio Effective One-Electron Potential Operators:Applications for Charge-Transfer Energy in Effective Fragment Potentials

The concept of effective one-electron potentials (EOP) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such asinteracting molecules in condensed phases. Here, a general method for EOP-based elimination of electronrepulsion integrals (ERIs) is presented, that is tuned towards the fragment-based calculation methodologiessuch as the second generation of the effective fragment potentials (EFP2) method. Two general types of theEOP operator matrix elements are distinguished and treated either via the distributed multipole expansion orthe extended density fitting schemes developed in this work. The EOP technique is then applied to reducethe high computational costs of the effective fragment charge-transfer (CT) terms being the bottleneck ofEFP2 potentials. The alternative EOP-based CT energy model is proposed, derived within the framework ofintermolecular perturbation theory with Hartree–Fock non-interacting reference wavefunctions, compatiblewith the original EFP2 formulation. It is found that the computational cost of the EFP2 total interactionenergy calculation can be reduced by up to 38 times when using the EOP-based formulation of CT energy,as compared to the original EFP2 scheme, without compromising the accuracy for a wide range of weaklyinteracting neutral and ionic molecular fragments. The proposed model can thus be used routinely withinthe EFP2 framework

Water Hydrogen-Bonding Network Structure and Dynamics at Phospholipid Multibilayer Surface: Femtosecond Mid-IR Pump-Probe Spectroscopy

The water hydrogen-bonding network at a lipid bilayer surface is crucial to understanding membrane structures and its functional activities. With a phospholipid multibilayer mimicking a biological membrane, we study the temperature dependence of water hydrogen-bonding structure, distribution, and dynamics at a lipid multibilayer surface using femtosecond mid-IR pump-probe spectroscopy. We observe two distinguished vibrational lifetime components. The fast component (0.6 ps) is associated with water interacting with a phosphate part, whereas the slow component (1.9 ps) is with bulk-like choline-associated water. With increasing temperature, the vibrational lifetime of phosphate-associated water remains constant though its relative fraction dramatically increases. The OD stretch vibrational lifetime of choline-bound water slows down in a sigmoidal fashion with respect to temperature, indicating a noticeable change of the water environment upon the phase transition. The water structure and dynamics are thus shown to be in quantitative correlation with the structural change of liquid multibilayer upon the gel-to-liquid crystal phase transition. © 2016 American Chemical Society112131sciescopu

Isonitrile as an Ultrasensitive Infrared Reporter of Hydrogen-Bonding Structure and Dynamics

Infrared (IR) probes based on terminally blocked beta-isocyanoalanine (AlaNC) and p-isocyanophenylalanine (PheNC) amino acids were synthesized. These isonitrile (NC)-derivatized compounds were extensively characterized by FTIR and femtosecond IR pump-probe spectroscopies, and a direct comparison was made with popularly used nitrile (CN)- and azide (N-3)-derivatized analogs. It is shown that the isonitrile stretch frequency exhibits extremely high sensitivity to hydrogen-bonding interactions. In addition, the IR intensity of the isonitrile group is much higher than that of the nitrile group and almost as intense as that of the azido group. Furthermore, its vibrational lifetime is much longer than that of the nitrile and azido groups. To elucidate the origin of such a high H-bond sensitivity and IR intensity observed for isonitrile, extensive quantum chemical calculations were performed. It is shown that the Coulombic contributions to the vibrational frequency shifts of the isonitrile and nitrile stretch modes have opposite signs but similar magnitudes, whereas the contributions of exchange repulsion and charge delocalization to their frequency shifts are comparable. Therefore, the isonitrile stretch frequency is much more sensitive to H-bonding interactions because the blue-shifting exchange-repulsion effects additionally enforced by such electrostatic effects. It is also shown that the much higher IR intensity of the isonitrile group compared to that of the nitrile group is due to the configuration reversal of the atomic electronegativity between the NC and CN groups. Owing to these features, we believe that isonitrile is a much better IR reporter of H-bonding structure and dynamics than the widely used nitrile and azide. © 2016 American Chemical Society111

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the “buried” probe site. This methodology should be widely applicable to vibrational probes in many environments. © XXXX American Chemical Societ

Unexpected solution phase formation of hollow PtSn alloy nanoparticles from Sn deposition on Pt dendritic structures

Hollow nanoparticles with a high surface-to-volume ratio have found various applications in catalysis, sensors, and energy storage, and thus new synthetic routes to these structures are of great interest. One of the best-known synthetic routes to hollow nanostructures is the utilization of the Kirkendall effect, which, however, is not useful for systems with a slow diffusing-out core such as Pt and fast diffusing-in surface elements such as Sn. Herein, we report a counterintuitive formation of hollow PtSn nanostructures by reacting dendritic Pt nanostructures with Sn precursors. © The Royal Society of Chemistry 20161111sciescopu

Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle

© 2019 American Chemical Society.The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interaction

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the “buried” probe site. This methodology should be widely applicable to vibrational probes in many environments