Search results for "Density Functional calculations"
showing 10 items of 56 documents
C2-Symmetric Ferrocene-Bis(ureido)peptides : Synthesis, Conformation and Solid-State Structure
2009
The extension of peptide derivatives of ferrocene-1,1'-dicarboxylic acid by formal insertion of NH units between ferrocene and peptide strands results in ferrocene-bis(ureido)-peptides. Experimentally, alanine and dialanine methyl esters were attached to the 1- and 1'-position of 1,1'-diiso-cyanoferrocene to give the corresponding bis(ureido)peptide derivatives 3 and 4. The conformation of 3 has been determined in the solid state by X-ray crystallography. In solution the preferred conformation of 3 and 4 has been elucidated by NMR, IR and CD spectroscopy in concert with DFT calculations. The secondary structure of ferrocene―bis(ureido)peptides 3 and 4 is determined by double bifurcated intr…
A DFT study of the molecular mechanisms of the nucleophilic addition of ester-derived lithium enolates and silyl ketene acetals to nitrones: Effects …
2006
9 pages, 6 schemes, 3 figures, 2 tables.
B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double…
2013
actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…
Advanced descriptors for long-range noncovalent interactions between SARS-CoV-2 spikes and polymer surfaces.
2021
The recent pandemic triggered numerous societal efforts aimed to control and limit the spread of SARS-CoV-2. One of these aspects is related on how the virion interacts with inanimate surfaces, which might be the source of secondary infection. Although recent works address the adsorption of the spike protein on surfaces, there is no information concerning the long-range interactions between spike and surfaces, experimented by the virion when is dispersed in the droplet before its possible adsorption. Some descriptors, namely the interaction potentials per single protein and global potentials, were calculated in this work. These descriptors, evaluated for the closed and open states of the sp…
Double-CO32− Centered [CoII5] Wheel and Modeling of Its Magnetic Properties
2010
A high-spin Co(II) cluster with a rare pentagonal molecular structure and formula [Co(5)(CO(3))(2)(bpp)(5)]ClO(4) (1; Hbpp is 2,6-bis(phenyliminomethyl)-4-methylphenolate) has been synthesized and characterized by single-crystal X-ray diffraction. This topology arises from fusing five [Co(2)(bpp)] moieties in a cyclic manner around two CO(3)(2-) central ligands, resulting in propeller-like configuration. The irregular coordination of the carbonate ions to the metal centers results in a combination of coordination numbers (CNs) of the Co(II) ions of five and six. The bulk magnetization of this complicated magnetically exchanged system has been modeled successfully by employing a matrix diago…
B‐DNA structure and stability: the role of nucleotide composition and order
2022
Abstract We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson–Crick base pairing, using dispersion‐corrected DFT at the BLYP‐D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better‐known eff…
Chalcogen‐Bonding Interactions in Telluroether Heterocycles [Te(CH2)m]n (n=1-4; m=3-7)
2020
The Te…Te secondary bonding interactions (SBI) in solid heterocyclic telluroethers were explored by preparing and structurally characterizing a series of [Te(CH2)m]n (n = 1‐4; m = 3‐7) species. The SBIs in 1,7‐Te2(CH2)10, 1,8‐Te2(CH2)12, 1,5,9‐Te3(CH2)9, 1,8,15‐Te3(CH2)18, 1,7,13,19‐Te4(CH2)20, 1,8,15,22‐Te4(CH2)24, and 1,9,17,25‐Te4(CH2)28 led to the tubular packing of the molecules, as has been observed previously for related thio‐ and selenoether rings. The nature of the intermolecular interactions was explored by solid‐state PBE0‐D3/pob‐TZVP calculations involving periodic boundary conditions. The packing of molecules in 1,7,13,19‐Te4(CH2)20, 1,8,15,22‐Te4(CH2)24, and 1,9,17,25‐Te4(CH2)…
Structure of superheavy nuclei along decay chains of element 115
2014
[Introduction] A recent high-resolution α , X -ray, and γ -ray coincidence-spectroscopy experiment offered the first glimpse of excitation schemes of isotopes along α -decay chains of Z = 115. To understand these observations and to make predictions about shell structure of superheavy nuclei below 288 115, we employ two complementary mean-field models: the self-consistent Skyrme energy density functional approach and the macroscopic-microscopic Nilsson model. We discuss the spectroscopic information carried by the new data. In particular, candidates for the experimentally observed E 1 transitions in 276 Mt are proposed. We find that the presence and nature of low-energy E 1 transitions in w…
A Tunable, Fullerene‐Based Molecular Amplifier for Vibrational Circular Dichroism
2019
Abstract Vibrational circular dichroism (VCD) studies are reported on a chiral compound in which a fullerene C60 moiety is used as an electron acceptor and local VCD amplifier for an alanine‐based peptide chain. Four redox states are investigated in this study, of which three are reduced species that possess low‐lying electronic states as confirmed by UV/Vis spectroelectrochemistry. VCD measurements in combination with (TD)DFT calculations are used to investigate (i) how the low‐lying electronic states of the reduced species modulate the amplification of VCD signals, (ii) how this amplification depends on the distance between oscillator and amplifier, and (iii) how the spatial extent of the…
From Mono- to Poly-Substituted Frameworks: A Way of Tuning the Acidic Character of C-c-H in o-Carborane Derivatives
2009
[EN] The incorporation of iodine atoms onto the boron vertices of the o-carborane framework causes, according to spectroscopic data, a uniform increase in the acidic character of the C-c-H (C-c= cluster carbon) vertices, whereas the incorporation of methyl groups onto the boron vertices of the o-carborane framework reduces their acidity. Methyl groups when attached to boron are electron-withdrawing in boron clusters, whereas iodine atoms bonded to boron act as electron donors. This has been proven on B-methyl and B-iodinated o-carboranes with NMR spectroscopy measurements and DFT calculations of natural bond orbital (NBO) charges. which show a Cumulative buildup of positive cluster only tot…