Journal ArticleDOI
Gas-phase spectroscopy of biomolecular building blocks.
TLDR
Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment in gas-phase spectroscopy.Abstract:
Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.read more
Citations
More filters
Journal ArticleDOI
DNA Excited-State Dynamics: From Single Bases to the Double Helix
Chris T. Middleton,Kimberly de La Harpe,Charlene Su,Yu Kay Law,Carlos E. Crespo-Hernández,Bern Kohler +5 more
TL;DR: Recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution are reviewed.
Journal ArticleDOI
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Jiří Šponer,Giovanni Bussi,Miroslav Krepl,Miroslav Krepl,Pavel Banáš,Sandro Bottaro,Richard A. Cunha,Alejandro Gil-Ley,Giovanni Pinamonti,Simón Poblete,Petr Jurečka,Nils G. Walter,Michal Otyepka +12 more
TL;DR: An in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods are covered.
Journal ArticleDOI
Progress and Challenges in the Calculation of Electronic Excited States
TL;DR: An overview of the ab initio quantum chemical and time-dependent density functional theory methods that can be used to model spectroscopy and photochemistry in molecular systems and three main applications that reflect the authors' experience are addressed.
Journal ArticleDOI
Spectroscopic studies of cold, gas-phase biomolecular ions
TL;DR: In this paper, a review presents a number of techniques employed in our laboratory and in others for measuring the spectroscopy of cold, gas-phase protonated peptides.
Journal ArticleDOI
Machine learning molecular dynamics for the simulation of infrared spectra
TL;DR: In this article, a molecular dipole moment model based on environment dependent neural network charges is proposed for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points.
References
More filters
Journal ArticleDOI
Numerical Recipes, The Art of Scientific Computing
Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
Brownian motion in a field of force and the diffusion model of chemical reactions
TL;DR: In this article, a particle which is caught in a potential hole and which, through the shuttling action of Brownian motion, can escape over a potential barrier yields a suitable model for elucidating the applicability of the transition state method for calculating the rate of chemical reactions.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Journal ArticleDOI
Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
Related Papers (5)
Getting into shape: Conformational and supramolecular landscapes in small biomolecules and their hydrated clusters
Evan G. Robertson,John P. Simons +1 more