Direct observation of ultrafast hydrogen bond strengthening in liquid water.
2021; 596 (7873): 531-535
Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network1, including unusually efficient vibrational energy redistribution and relaxation2. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04A on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.
View details for DOI 10.1038/s41586-021-03793-9
View details for PubMedID 34433948
- Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water CHEMICAL SCIENCE 2021
Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model.
Journal of chemical theory and computation
We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.
View details for DOI 10.1021/acs.jctc.0c01323
View details for PubMedID 34009969
- Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy CHEMICAL SCIENCE 2020; 11 (16): 4180–93
Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems.
The Journal of chemical physics
2020; 152 (21): 214115
The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
View details for DOI 10.1063/1.5144298
View details for PubMedID 32505165
Beyond the electric-dipole approximation in simulations of x-ray absorption spectroscopy: Lessons from relativistic theory.
The Journal of chemical physics
2020; 152 (18): 184110
We present three schemes to go beyond the electric-dipole approximation in x-ray absorption spectroscopy calculations within a four-component relativistic framework. The first is based on the full semi-classical light-matter interaction operator and the two others on a truncated interaction within the Coulomb gauge (velocity representation) and multipolar gauge (length representation). We generalize the derivation of the multipolar gauge to an arbitrary expansion point and show that the potentials corresponding to different expansion points are related by a gauge transformation, provided that the expansion is not truncated. This suggests that the observed gauge-origin dependence in the multipolar gauge is more than just a finite-basis set effect. The simplicity of the relativistic formalism enables arbitrary-order implementations of the truncated interactions, with and without rotational averaging, allowing us to test their convergence behavior numerically by comparison to the full formulation. We confirm the observation that the oscillator strength of the electric-dipole allowed ligand K-edge transition of TiCl4, when calculated to the second order in the wave vector, becomes negative but also show that inclusion of higher-order contributions allows convergence to the result obtained using the full light-matter interaction. However, at higher energies, the slow convergence of such expansions becomes dramatic and renders such approaches at best impractical. When going beyond the electric-dipole approximation, we therefore recommend the use of the full light-matter interaction.
View details for DOI 10.1063/5.0003103
View details for PubMedID 32414251
- VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019