Search results for "molekyylit"

Computational investigations on rotational and vibrational spectroscopies of some diatomics in solid environment

2013

In this thesis, spectroscopic and structural properties of homogeneous para-hydrogen crystals and diatomic molecules embedded in rare gas crystals are explored by theoretical means. The agreement with experimental signatures indicates the suitability of the chosen quantum and classical methods to accurately describe the various low-temperature physical and chemical problems investigated at the laser laboratory. A novel explanation of band structures in Raman and IR spectra is given for CO in Ar. Rotational transition rules are found to dictate the spectral broadening of infrared and Raman band structures as a function of temperature. The results show that after photodissociation of matrix-i…

Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule-Cavity Systems

2022

The strong light–matter coupling regime, in which excitations of materials hybridize with excitations of confined light modes into polaritons, holds great promise in various areas of science and technology. A key aspect for all applications of polaritonic chemistry is the relaxation into the lower polaritonic states. Polariton relaxation is speculated to involve two separate processes: vibrationally assisted scattering (VAS) and radiative pumping (RP), but the driving forces underlying these two mechanisms are not fully understood. To provide mechanistic insights, we performed multiscale molecular dynamics simulations of tetracene molecules strongly coupled to the confined light modes of an…

Large Azobenzene Macrocycles : Formation and Detection by NMR and MS Methods

2023

Azobenzene macrocycles are widely investigated as potential drug delivery systems and as part of molecular machines due to their photo-responsive properties. Herein, we detect the formation of a series of new azobenzene macrocycles that feature up to eight switchable repeating units. High-resolution mass spectrometry and ion mobility (IM) mass spectrometry experiments and 1H and diffusion-ordered spectroscopy (DOSY) NMR are used to detect the presence of the macrocycles that contain 10 to 40 aromatic rings in the gas phase and solution, respectively. The responsiveness of the Z-to-E photo-switching of the smallest of the macrocycles, exhibiting two azobenzene units and in total 10 aromatic …

Molekyylien linjautuminen laserkentässä

2009

Stability, electronic structure, and optical properties of protected gold-doped silver Ag29-xAux (x = 0-5) nanoclusters

2017

In this work, we used density functional theory (DFT) and linear response time-dependent DFT (LR-TDDFT) to investigate the stability, electronic structure, and optical properties of Au-doped [Ag29−xAux(BDT)12(TPP)4]3− nanoclusters (BDT: 1,3-benzenedithiol; TPP triphenylphosphine) with x = 0–5. The aim of this work is to shed light on the most favorable doped structures by comparing our results with previously published experimental data. The calculated relative energies, ranging between 0.8 and 10 meV per atom, indicate that several doped Ag29−xAux nanoclusters are likely to co-exist at room temperature. However, only the Au-doped [Ag29−xAux(BDT)12(TPP)4]3− nanoclusters that have direct bon…

Metabolic plasticity of mixotrophic algae is key for their persistence in browning environments

2022

Light availability is the main regulator of primary production, shaping photosynthetic communities and their production of ecologically important biomolecules. In freshwater ecosystems, increasing dissolved organic carbon concentrations, commonly known as browning, leads to lower light availability and the proliferation of mixotrophic phytoplankton. Here, a mixotrophic algal species (Cryptomonas sp.) was grown under five increasing dissolved organic carbon concentrations to uncover the plastic responses behind the success of mixotrophs in browning environments and their effect in the availability of nutritionally important biomolecules. In addition to the browning treatments, phototrophic, …

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

2022

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on…

Pintaplasmonipolaritonien ja molekyylien väliset energiansiirtoprosessit ja dynamiikka

2012

Computational studies of biomolecular screening and interactions

2015

isotracer: An R package for the analysis of tracer addition experiments

2022

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging. We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, inc…