Search results for "Ab initio"

NMR structure determination of (11E)-trinervita-1(14),2,11-triene, a new diterpene from sexual glands of termites

2005

Graphical Abstract Full-size image; International audience; Female alates of Nasutitermes ephratae termites from Guadeloupe and Nasutitermes sp. from Brazil produce a diterpene hydrocarbon of the molecular formula C20H30 as the main component of their tergal gland secretion. Analysis of NMR, IR, and mass spectra of the diterpene led to a structure of (11E)-trinervita-1(14),2,11-triene. Based on a comparison with the published oxygenated trinervitane skeleton from termites we prefer the enantiomer with absolute configurations (4R,7S,8R,15S,16S). The suggested structure is supported by ab initio quantum chemical calculation of 1H and 13C chemical shifts for the optimized geometry of the molec…

panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.

2018

Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…

Permeability of three-dimensional random fiber webs

1998

We report the results of essentially ab initio simulations of creeping flow through large threedimensional random fiber webs that closely resemble fibrous sheets such as paper and nonwoven fabrics. The computational scheme used in this Letter is that of the lattice-Boltzmann method and contains no free parameters concerning the properties of the porous medium or the dynamics of the flow. The computed permeability of the web is found to be in good agreement with experimental data, and confirms that permeability depends exponentially on porosity over a large range of porosity. [S0031-9007(97)05087-4]

Quantum-chemical determination of Born–Oppenheimer breakdown parameters for rotational constants: the open-shell species CN, CO+ and BO

2013

The quantum-chemical protocol for computing Born-Oppenheimer breakdown corrections to rotational constants in the case of diatomic molecules is extended to open-shell species. The deviation from the Born-Oppenheimer equilibrium rotational constant is obtained by considering three contributions: the adiabatic correction to the equilibrium bond distance, the electronic contribution to the moment of inertia requiring the computation of the rotational g-tensor, and the so-called Dunham correction. Values for the Born-Oppenheimer breakdown parameters of CN, CO+, and BO in their (2)sigma(+) electronic ground states are reported based on coupled-cluster calculations of the involved quantities and …

Ab initio calculations of pure and Co+2-doped MgF2 crystals

2020

This research was partly supported by the Kazakhstan Science Project № AP05134367«Synthesis of nanocrystals in track templates of SiO2/Si for sensory, nano- and optoelectronic applications», as well as by Latvian Research Council project lzp-2018/1-0214. Calculations were performed on Super Cluster (LASC) in the Institute of Solid State Physics (ISSP) of the University of Latvia. Authors are indebted to S. Piskunov for stimulating discussions.

H-He collision-induced satellite in the Lyman alpha profile of DBA white dwarf stars

2020

The spectra of helium-dominated white dwarf stars with hydrogen in their atmosphere present a distinctive broad feature centered around 1160~\AA\/ in the blue wing of the Lyman-$\alpha$ line. It is extremely apparent in WD 1425+540 recently observed with HST COS. With new theoretical line profiles based on ab initio atomic interaction potentials we show that this feature is a signature of a collision-induced satellite due to an asymptotically forbidden transition. This quasi-molecular spectral satellite is crucial to understanding the asymmetrical shape of Lyman-$\alpha$ seen in this and other white dwarf spectra. Our previous work predicting this absorption feature was limited by molecular…

Theoretical study of photoinduced ring-isomerization in the 1,2,4-oxadiazole series

2004

Abstract A theoretical study of photoinduced ring-isomerization of 3-amino-5-methyl- and 3-amino-5-phenyl-1,2,4-oxadiazoles is reported. The results well agree with the reported experimental data: in particular, they explain the ring-photoisomerization into the corresponding 2-amino-1,3,4-oxadiazoles through a ring contraction-ring expansion route; moreover, the occurrence of competing pathways involving both the ring contraction and the internal cyclization–isomerization mechanism during irradiation of the 5-alkyl substituted substrates in the presence of a base has been also substantiated.

Reply to Comment on “Mixed Grotthuss and Vehicle Transport Mechanism in Proton Conducting Polymers from Ab initio Molecular Dynamics Simulations”

2011

Magic triangular and tetrahedral clusters

1997

Using the methods of density functional theory and the jellium model we show that clusters with triangular [in two dimensions (2D)] or tetrahedral [in three dimensions (3D)] shapes have a strong shell structure and enhanced stability. Moreover, the shell closings correspond to the lowest magic numbers of a 2D and 3D harmonic oscillator and at the same time to the number of divalent atoms in close-packed triangles and tetrahedrons. Ab initio molecular dynamics simulations for Na and Mg clusters support the results of the jellium model.

Revisiting the Nonadiabatic Process in 1,2-Dioxetane.

2015

Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurati…