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CPPE: An Open-Source C++ and Python Library for Polarizable Embedding
(Journal article; Tidsskriftartikkel; Peer reviewed, 2019-10-03)We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been ... -
Critical Assessment of Metagenome Interpretation: the second round of challenges
(Journal article; Tidsskriftartikkel; Peer reviewed, 2022-04-08)Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids ... -
Cryptic β-Lactamase Evolution Is Driven by Low β-Lactam Concentrations
(Journal article; Tidsskriftartikkel; Peer reviewed, 2021-04-28)Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the widespread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to developing clinical resistance. Here, we subjected <i>Escherichia ... -
Cryptophanes for Methane and Xenon Encapsulation: A Comparative Density Functional Theory Study of Binding Properties and NMR Chemical Shifts
(Journal article; Tidsskriftartikkel; Peer reviewed, 2017-11-27)The host-guest chemistry of cryptophanes is an active research area because of its applications in sensor design, targeting small molecules and atoms in environmental and medical sciences. As such, the computational prediction of binding energies and nuclear magnetic resonance (NMR) properties of different cryptophane complexes are of interest to both theoreticians and experimentalists ... -
Crystal Structure Evolution of Fluorine under High Pressure
(Journal article; Tidsskriftartikkel; Peer reviewed, 2022-07-01)Fluorinated compounds in the last decade were applied as photothermo-refractive glasses, high-stress lubricants, and pharmaceutical drugs due to their good mechanical properties and biocompatibility. Although fluorinated materials are largely employed, the possibility of predicting new structures was limited by the impossibility to use density functional theory (DFT) to describe interatomic ... -
The crystal structure of haemoglobin from Atlantic cod
(Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-16)The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 A˚ resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly. -
Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans
(Journal article; Tidsskriftartikkel, 2015-02-27)Background: Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding ... -
The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-02-29)L‐2,4‐diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω‐position of substrates, and is the intial and rate‐limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)‐2‐methyl‐1,4,5,6‐tetrahydro‐4‐pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases ... -
Cyclic Voltammetric Study of 2-Hydroxybenzophenone (HBP) Derivatives and the Correspondent Change in the Orbital Energy Levels in Different Solvents
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-14)The experimental UV and CV of five substituted 2-hydroxybenzophenones in solvents acetonitrile, n-dimethylformamide and dimethylsulfoxide are presented. Results obtained were used to determine their experimental highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and the results were compared to their theoretical model. The derivatives with an electron withdrawing ... -
D3.3 (M18) - Report on curation in core ELIXIR registries (an ELIXIR Norway ELIXIR3 deliverable)
(Research report; Forskningsrapport, 2023-10-01)This report serves as an update on the progress of WP3 Task 3.4 in ELIXIR3, in support of curation efforts on content in repositories of metadata, datasets, tools, training, workflows, and other resources, in line with the ELIXIR Platforms. The report documents progress made, methods used, and plans for the near future as of month 18 of a 48-month timeline. ELIXIR Norway extends support to numerous ... -
Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-05)The <i>Dalton Project</i> 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 Dalton quantum chemistry program system
(Journal article; Tidsskriftartikkel; Peer reviewed, 2014-05)Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self-consistent-field, Møller–Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients ... -
Darmstadtium, roentgenium, and copernicium form strong bonds with cyanide
(Journal article; Tidsskriftartikkel; Peer reviewed, 2017-05-05)We report the structures and properties of the cyanide complexes of three superheavy elements (darmstadtium, roentgenium, and copernicium) studied using two‐ and four‐component relativistic methodologies. The electronic and structural properties of these complexes are compared to the corresponding complexes of platinum, gold, and mercury. The results indicate that these superheavy elements form ... -
Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR
(Journal article; Tidsskriftartikkel; Peer reviewed, 2017-07-04)Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive data begin to enable design against a spectrum of targets (polypharmacology); however, the data also reveal heterogeneities of structure, subtleties of chemical interactions, and apparent inconsistencies ... -
Data to Understand the Nature of Non-Covalent Interactions in the Thiophene Clusters
(Journal article; Tidsskriftartikkel; Peer reviewed, 2022-01-10)We have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we have also provided the optimized Cartesian coordinates of all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to ... -
A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges
(Journal article; Tidsskriftartikkel; Peer reviewed, 2016-04-27)The Deinococcus radiodurans bacterium is extremely resistant to ionising radiation and desiccation and can withstand a 200-fold higher radiation dose than most other bacteria with no loss of viability. The mechanisms behind this extreme resistance are not fully understood, but it is clear that several factors contribute to this phenotype. Efficient scavenging of reactive oxygen species and repair ... -
Degradation of oil products in a soil from a Russian Barents hot‑spot during electrodialytic remediation
(Journal article; Tidsskriftartikkel; Peer reviewed, 2016-02-24)A highly oil-polluted soil from Krasnoe in North-West Russia was used to investigate the degradation of organic pollutants during electrodialytic remediation. Removal efficiencies were up to 70 % for total hydrocarbons (THC) and up to 65 % for polyaromatic hydrocarbons (PAH). Relatively more of the lighter PAH compounds and THC fractions were degraded. A principal component analysis (PCA) revealed ... -
Demetalation of copper undecaarylcorroles: Molecular structures of a free-base undecaarylisocorrole and a gold undecaarylcorrole
(Journal article; Tidsskriftartikkel; Peer reviewed, 2016-06-27)Copper undecaarylcorroles were found to undergo acid-induced demetalation with unusual ease under both reductive and nonreductive conditions. The resulting free-base undecaarylcorroles were found to be rather reactive, readily photooxygenating to yield 5/10-hydroxyisocorroles and open-chain tetrapyrroles. The use of nonreductive conditions led to 50-75% yields of undecaarylisocorroles, a new class ... -
Demystifying the Origin of Vibrational Coherence Transfer Between the S1 and T1 States of the Pt-pop Complex
(Journal article; Tidsskriftartikkel; Peer reviewed, 2021-10-01)We demonstrate that spin-vibronic coupling is the most significant mechanism in vibrational coherence transfer (VCT) from the singlet (S<sub>1</sub>) to the triplet (T<sub>1</sub>) state of the [Pt<sub>2</sub>(P<sub>2</sub>O<sub>5</sub>H<sub>2</sub>)<sub>4</sub>]<sup>4–</sup> complex. Our time-dependent correlation function-based study shows that the rate of intersystem crossing (<i>k</i><sub>ISC</sub>) ... -
Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization
(Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-25)Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine ...