Search results for "molekyylit"

Complexes of Glycolic Acid with Nitrogen Isolated in Argon Matrices. II : Vibrational Overtone Excitations

2019

Structural changes of glycolic acid (GA) complex with nitrogen induced by selective overtone excitation of the νOH mode were followed in argon matrices using FTIR spectroscopy. For the most stable SSC1 complex present in different trapping sites directly upon deposition site, selective changes in the νOH region were achieved upon near-infrared irradiation. Simultaneously, new conformers of the GA…N2 complex were formed, giving rise to several sets of bands in the νOH and νC=O regions of the spectra. Both position and intensity of new absorptions appeared to be highly sensitive on the wavelength of radiation used, as well as on the annealing of the matrix. Based on theoretical calculations a…

Synthesis, characterization, and reactivity of heavier group 13 and 14 metallylenes and metalloid clusters : small molecule activation and more

2015

Polymer dynamics in time-dependent periodic potentials.

2008

Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations for computing the stationary state properties of molecules with internal structure in time-dependent periodic potentials on a lattice. As an example, we consider standard and modified Rubinstein-Duke polymers and calculate their mean drift and effective diffusion coefficient in the two-state non-symmetric flashing potential and symmetric traveling potential. Rich non-linear behavior of these observables is found. By varying the polymer length, we find cur…

Strictly correlated electrons approach to excitation energies of dissociating molecules

2019

In this work we consider a numerically solvable model of a two-electron diatomic molecule to study a recently proposed approximation based on the density functional theory of so-called strictly correlated electrons (SCE). We map out the full two-particle wave function for a wide range of bond distances and interaction strengths and obtain analytic results for the two-particle states and eigenenergies in various limits of strong and weak interactions, and in the limit of large bond distance. We then study the so-called Hartree-exchange-correlation (Hxc) kernel of time-dependent density functional theory which is a key ingredient in calculating excitation energies. We study an approximation b…

Binding of ion pairs and neutral guests by aryl-extended meso‑p-hydroxyphenyl calix[4]pyrrole : The interplay between three binding sites

2023

An aryl-extended calix[4]pyrrole with four meso‑p-hydroxyphenyl substituents was investigated as a host for chloride, acetate, and benzoate anions. Crystal structures of pyridinium and imidazolium chloride complexes were obtained in which chloride ions are hydrogen bonded exo-cavity to the upper rim hydroxyl groups, and the aromatic cations are bound to the shallow cavity of the host. Furthermore, the calix[4]pyrrole formed a hydrogen bonded dimeric capsule templated by inclusion of adiponitrile guest in the endo-cavity binding site. NMR titrations revealed the preference of the OH groups of the host to bind anionic guests in solution. Benzoate anion had the highest binding constant (4 700 …

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…

Many-particle approach to lead-molecule interactions and to the image-charge effect

2011

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…

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, …

Raman spectroscopy of glycolic acid complexes with N2

2019

High overtone excitation induced conformational isomerization of glycolic acid – nitrogen complex in an argon matrix was investigated by Raman spectroscopy. The interaction between glycolic acid and nitrogen change the green light (532 nm) induced isomerization processes compared to non-complexed glycolic acid. The 180° rotation around of the Csingle bondC bond and stabilization of carboxyl Odouble bondCsingle bondOsingle bondH dihedral angle to trans position were the main conformational changes observed in the complex of the lowest energy conformer and nitrogen. Interestingly, only one stable light-induced conformational product was observed, which isomerises back to the lowest energy con…