Search results for "functional"

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…

Computational Analysis of n→π* Back-Bonding in Metallylene–Isocyanide Complexes R2MCNR′ (M = Si, Ge, Sn; R = tBu, Ph; R′ = Me, tBu, Ph)

2013

A detailed computational investigation of orbital interactions in metal–carbon bonds of metallylene–isocyanide adducts of the type R2MCNR′ (M = Si, Ge, Sn; R, R′ = alkyl, aryl) was performed using density functional theory and different methods based on energy decomposition analysis. Similar analyses have not been carried out before for metal complexes of isocyanides, even though the related carbonyl complexes have been under intense investigations throughout the years. The results of our work reveal that the relative importance of π-type back-bonding interactions in these systems increases in the sequence Sn < Ge ≪ Si, and in contrast to some earlier assumptions, the π-component cannot be …

Substituent effects on axle binding in amide pseudorotaxanes: comparison of NMR titration and ITC data with DFT calculations

2012

The binding behaviour of differently substituted diamide axle molecules to Hunter/Vögtle tetralactam macrocycles was studied with a combination of NMR titration, isothermal titration calorimetry (ITC) experiments and calculations employing density functional theory (DFT), along with dispersion-corrected exchange-correlation functionals. Guests with alkyl or alkenyl chains attached to the diamide carbonyl groups have a significantly higher binding affinity to the macrocycle than guests with benzoyl amides and their substituted analogues. While the binding of the benzoyl and alkenyl substituted axles is enthalpically driven, the alkyl-substituted guest binds mainly because of a positive bindi…

The role of the transfer group in the intramolecular [5+2] cycloadditions of substituted β-hydroxy-γ-pyrones: a DFT analysis

2005

The intramolecular [5+2] cycloaddition reactions of a series of 3-OR (R=SiMe3, H, CHO, Me) substituted β-hydroxy-γ-pyrones bearing tethered alkenes were studied using DFT methods at the B3LYP/6–31G* level. The role of the transfer R group was analyzed considering two alternative channels: (i) in channel a the process is initialized by the transfer of the R group with formation of an oxidopyrylium ylide intermediate, which is followed of an intramolecular [5+2] cycloaddition; (ii) in channel b, the process is initialized by the intramolecular [5+2] cycloaddition on the γ-pyrone followed by the transfer of the R group. Copyright © 2005 John Wiley & Sons, Ltd.

Gold(iii) tetraarylporphyrin amino acid derivatives: ligand or metal centred redox chemistry?

2015

EPR spectroscopy and DFT calculations show that the site of reduction of porphyrinato gold(iii) complexes depends on the counterions X, the meso substituents R and the solvent.

Conformation of tert-butoxycarbonylglycyl-dehydroalanyl-glycine methyl ester in the crystalline state and calculated in the gas phase.

2006

tert-Butoxy­carbonyl­glycyl-dehydro­alanyl-glycine methyl ester (systematic name: methyl {2-[(tert-butoxycarbonylamino)­acetamido]prop-2-enamido}acetate) (Boc0-Gly1-ΔAla2-Gly3-OMe), C13H21N3O6, has been structurally characterized by single-crystal X-ray diffraction and by density functional theory (DFT) calculations at the B3LYP/6–311+G** level. The peptide chain in both the solid-state and calculated structures adopts neither β nor γ turns. All amino acid residues in the tripeptide sequence are linked trans to each other. The bond lengths and valence angles of the amino acid units in the crystal structure and gas phase are comparable. However, the conformation of the third glycyl residue (…

Nonlocal van der Waals Approach Merged with Double-Hybrid Density Functionals: Toward the Accurate Treatment of Noncovalent Interactions

2015

Noncovalent interactions drive the self-assembly of weakly interacting molecular systems to form supramolecular aggregates, which play a major role in nanotechnology and biochemistry. In this work, we present a thorough assessment of the performance of different double-hybrid density functionals (PBE0-DH-NL, revPBE0-DH-NL, B2PLYP-NL, and TPSS0-DH-NL), as well as their parent hybrid and (meta)GGA functionals, in combination with the most modern version of the nonlocal (NL) van der Waals correction. It is shown that this nonlocal correction can be successfully coupled with double-hybrid density functionals thanks to the short-range attenuation parameter b, which has been optimized against ref…

Studies towards the development of lipophilic bifunctional N3S3 chelators for 68Ga

2010

Abstract The present study is concerned with a concept of charge-neutral, lipophilic, macrocyclic bifunctional chelators, suitable for the introduction of a gallium-68 label into small molecules. The synthesis of a novel bifunctional N3S3-type chelator, derived from 1,4,7-triazacyclononane, initial 68Ga-radiolabelling and the determination of stability and calculated lipophilicity of the compound are described. The 68Ga-labelled chelate was obtained in a maximum radiochemical yield of 93±5% after a reaction time of 2 min. It remained intact over 3 h in a DTPA-challenge and a transferrin challenge experiment, indicating sufficient stability for PET studies.

ChemInform Abstract: First Evidence of Proline Acting as a Bifunctional Catalyst in the Baylis-Hillman Reaction Between Alkyl Vinyl Ketones and Aryl …

2008

Proline in the presence of sodium hydrogen carbonate has been found to be an effective catalyst for the Baylis–Hillman reaction between methyl or ethyl vinyl ketone and aryl aldehydes. Screening of several amine catalysts showed that an ionizable carboxylic function directly linked to the secondary amine catalyst plays an important role in the synthesis of the desired product in good yield. The data obtained has allowed us to suggest, for the first time, that proline, sarcosine, pipecolinic acid and homoproline may act as bifunctional catalysts via a bicyclic enaminolactone species as intermediate. Quantum-mechanical calculations (PM3/COSMO and ab initio 3-21G/COSMO) support this mechanism …

1992

A series of copolymers are synthesized by repetitive Diels-Alder polyaddition reaction of bifunctional cyclohepta-1,3,5-trienes with bifunctional 1,2,4-triazoline-3,5-diones. The copolymers of different bistriazolinediones with a bisdiene, or of different biscycloheptatrienes with a dienophile, have good solubility in CH2Cl2 and CHCl3, while the homopolymers are poorly soluble. The copolymers were characterized by standard analytical techniques to test the structural regularity of these systems. Due to the kinetic control, it is possible to apply copolymerization statistics to these systems. Based on a model study, it is concluded that alipatic and aromatic bistriazolinediones have the same…