Search results for "DFT"

Toward engineering efficient peptidomimetics. Screening conformational landscape of two modified dehydroaminoacids

2013

Effective peptidomimetics should posses structural rigidity and appropriate interaction pattern leading to potential spatial and electronic matching to the target receptor site. Rational design of such small bioactive molecules could push chemical synthesis and molecular modeling toward faster progress in medicinal chemistry. Conformational properties of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′,N′-dimethylamides (Boc-Gly-(E/Z)-ΔPhe-NMe2) in chloroform were studied by NMR and IR spectroscopy. The experimental findings were supported by extensive calculations at DFT(B3LYP, M06-2X) and MP2 levels of theory and the β-turn tendency for both isomers of the studied dipeptide were d…

Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

2011

Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral …

Hydrogen activation on N‐doped carbon networks

2014

Aromaticity and planarity of zinc phthalocyanine (ZnPc) characterized by splitting of NICS(1) index

2018

The planarity of zinc phthalocyanine (ZnPc) in the gas phase and water, with solute-solvent interactions modeled by polarized continuum model (PCM), has been characterized with new indexes of aromaticity. The aromaticity of individual ring subunits of ZnPc molecule was studied on the basis of nucleus independent chemical shift index (NICS) above and below the molecular plane. Density functional theory (DFT) with selected Pople-type basis sets was used to study the local aromaticity. The calculated NICS(1) and NICS(-1) indexes of aromaticity for a non-planar ZnPc molecule in the polar environment are significantly different.

Method and basis set dependence of the NICS indexes of aromaticity for benzene

2018

The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3 ppm. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent o…

Ag44(SeR)30: A Hollow Cage Silver Cluster with Selenolate Protection.

2015

Selenolate protected, stable and atomically precise, hollow silver cluster was synthesized using solid state as well as solution state routes. The optical absorption spectrum shows multiple and sharp features similar to the thiolated Ag44 cluster, Ag44(SR)30 whose experimental structure was reported recently. High-resolution electrospray ionization mass spectrometry (HRESI MS) shows well-defined molecular ion features with two, three, and four ions with isotopic resolution, due to Ag44(SePh) 30. Additional characterization with diverse tools confirmed the composition. The closed-shell 18 electron superatom electronic structure, analogous to Ag44(SR)30 stabilizes the dodecahedral cage with a…

A continuum damage model for functionalized graphene membranes based on atomistic simulations

2017

A continuum model for GO membranes is developed in this study. The model is built representing the membrane as a two-dimensional, heterogeneous, two-phase continuum and the constitutive behavior of each phase (graphitic or oxidized) is built based on DFTB simulations of representative patches. A hyper-elastic continuum model is employed for the graphene areas, while a continuum damage model is more adequate for representing the behavior of oxidized regions. A finite element implementation for GO membranes subjected to degradation and failure is then implemented and, to avoid localization instabilities and spurious mesh sensitivity, a simple crack band model is adopted. The developed impleme…

Structure-Directing and High-Efficiency Photocatalytic Hydrogen Production by Ag Clusters

2014

H2 production by water splitting is hindered mainly by the lack of low-cost and efficient photocatalysts. Here we show that sub-nanometric silver clusters can catalyze the anisotropic growth of gold nanostructures by preferential adsorption at certain crystal planes of Au seeds, with the result that the final nanostructure can be tuned via the cluster/seed ratio. Such semiconducting Ag clusters are extremely stable and retain their electronic structure even after adsorption at the tips of Au nanorods, enabling various photocatalytic experiments, such as oxygen evolution from basic solutions. In the absence of electron scavengers, UV irradiation generates photoelectrons, which are stored wit…

AB Initio Calculations of CUN@Graphene (0001) Nanostructures for Electrocatalytic Applications

2018

Funding from European Union’s Horizon 2020 Research and Innovation Programme project under grant agreement No. 768789 is greatly acknowledged.

OH-functionalized open-ended armchair single-wall carbon nanotubes (SWCNT) studied by density functional theory

2011

The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 A for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol−1) reactive toward hydroxylation. Figure The structures of ide…