In this study, a sensing device employing gold-coated quartz tuning fork (QTF) modified with self-assembled monolayer (SAM) of L-cysteine was evaluated for the sensitive detection Cu2+ ions in aqueous solutions. Three copper (II) salts, CuSO4, CuCl2, and Cu(NO3)2, at four different concentrations (10−12, 10−10, 10−8, 10−6 M) small (100 μL) water sample amounts were each used as analytes to inve...

Density functional theory (DFT) has provided deep atomic-level insights into the adsorption behavior of aromatic molecules on solid surfaces. However, modeling surface phenomena large mineral surfaces with accurate plane wave methods (PW) can be orders magnitude more computationally expensive than localized atomic orbitals (LCAO) methods. In present work, we propose a less costly approach based...

Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bimetallic Mg(II)/Zn(II) enzyme, isopentenyl diphosphate isomerase, to an inhibitor built up of a trianionic diphosphate and of a cationic ethyldimethylammonium (EDMA) moiety. The analyses are performed on the protein recognition site, which totals 13 residues, as well as on some "mutants" in which one...

Geometries, vibrational frequencies, and interaction energies of the CNH ̄O3 and HCCH ̄O3 complexes are calculated in a counterpoise-corrected ~CP-corrected! potential-energy surface ~PES! that corrects for the basis set superposition error ~BSSE!. Ab initio calculations are performed at the Hartree–Fock ~HF! and second-order Mo”ller–Plesset ~MP2! levels, using the 6-31G(d ,p) and D9511(d ,p) bas...

Attenuated second-order Møller-Plesset perturbation theory (MP2) within the finite aug-cc-pVTZ (aTZ) basis set is developed for inter- and intra-molecular non-bonded interactions. A single attenuation parameter is optimized on the S66 database of 66 intermolecular interactions, leading to a very large RMS error reduction by a factor of greater than 5 relative to standard MP2/aTZ. Attenuation in...

As a result of research on ligand efficiency in the pharmaceutical industry, there is greater focus on optimizing the strength of polar interactions within receptors, so that the contribution of overall size and lipophilicity to binding can be decreased. A number of quantum mechanical (QM) methods involving simple probes are available to assess the H-bonding potential of different heterocycles ...

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show tha...

As High Content Screening (HCS) has moved into the main stream for biological and pharmaceutical investigations, a lag of well integrated pipelines for automated acquisition, management and analysis of HCS results turns out to be a bottleneck for fully leveraging the wealth of information contained in a screen and moving to higher throughput. For many applications, monolithic pipelines can not ...

Local stretching modes for 69 different DH single bonds and 58 H· · ·A H-bonds are calculated at the ωB97X-D/aug-cc-pVTZ level of theory to describe the changes in donor D and acceptor A upon forming the hydrogen-bonded complex. The intrinsic strength of the DH and AH interactions is determined utilizing the properties of a well-defined set of local, uncoupled vibrational modes. The local mode ...

We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation...