Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO2, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO2 or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO2) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question

Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin—an insight from molecular dynamics simulations with classical and ab initio force fields

In the field of enzymatic catalysis, creating activity from a non catalytic scaffold is a daunting task. Introduction of a catalytically active moiety within a protein scaffold offers an attractive means for the creation of artificial metalloenzymes. With this goal in mind, introduction of a biotinylated d6-piano-stool complex within streptavidin (SAV) affords enantioselective artificial transfer-hydrogenases for the reduction of prochiral ketones. Based on an X-ray crystal structure of a highly selective hybrid catalyst, displaying significant disorder around the biotinylated catalyst [η6-(p-cymene)Ru(Biot-p-L)Cl], we report on molecular dynamics simulations to shed light on the protein–cofactor interactions and contacts. The results of these simulations with classical force field indicate that the SAV-biotin and SAV-catalyst complexes are more stable than ligand-free SAV. The point mutations introduced did not affect significantly the overall behavior of SAV and, unexpectedly, the P64G substitution did not provide additional flexibility to the protein scaffold. The metal-cofactor proved to be conformationally flexible, and the S112K or P64G mutants proved to enhance this effect in the most pronounced way. The network of intermolecular hydrogen bonds is efficient at stabilizing the position of biotin, but much less at fixing the conformation of an extended biotinylated ligand. This leads to a relative conformational freedom of the metal-cofactor, and a poorly localized catalytic metal moiety. MD calculations with ab initio potential function suggest that the hydrogen bonds alone are not sufficient factors for full stabilization of the biotin. The hydrophobic biotin-binding pocket (and generally protein scaffold) maintains the hydrogen bonds between biotin and protein

Molecular Property Investigations of an ortho-Hydroxy Schiff Base Type Compound with the First-Principle Molecular Dynamics Approach

The structure, proton transfer, and vibrational dynamics Under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(N-methyl-alpha-iminoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized in the nitrogen side of the O center dot center dot center dot H center dot center dot center dot N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while I more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects in this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR Spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1) assigned to the labile proton. In mere Contrast, a much more localized absorption band around 2600-2700 cm(-1) is predicted in the crystal phase. Finally, effects of the quantization of the proton motion in the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (ID) potential energy surface (PES) for the proton along the O center dot center dot center dot H center dot center dot center dot N bridge in a vacuum. The ID Schrodinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal

Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases-A comparative molecular dynamics study

We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O ... N)) <= 2.6 angstrom), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects. (C) 2011 American Institute of Physics. [doi:10.1063/1.3528721

Investigation of 6-fluoroquinolones activity against Mycobacterium tuberculosis using theoretical molecular descriptors: a case study

<p>A quantitative structure-activity relationship (QSAR) study on a set of 66 structurally-similar 6-fluoroquinolones was performed using a large pool of theoretical molecular descriptors. Ab initio geometry optimizations were carried out to reproduce the geometrical and electronic structure parameters. The resulting molecular structures were confirmed to be minima via harmonic frequency calculations. Obtained atomic charges, HOMO and LUMO energies, orbital electron densities, dipole moment, energy and many other properties served as quantum-chemical descriptors. A multiple linear regression (MLR) technique was applied to generate a linear model for predicting the biological activity, Minimal Inhibitory Concentration (MIC), treated as negative decade logarithm, (pMIC). The heuristic method was used to optimize the model parameters and select the most significant descriptors. The model was tested internally using the CV LOO procedure on the training set and validated against the external validation set. The result (Q 2 ext = 0.7393), which was obtained on an external, previously excluded validation data set, shows the predictive performances of this model (R 2 tr = 0.7416, Q 2 tr = 0.6613) in establishing (Q)SAR of 6-fluoroquinolones. This validated model could be proficiently used to design new 6-fluoroquinolones with possible higher activity.</p

Hydrogen Bonding as a Modulator of Aromaticity and Electronic Structure of Selected <i>ortho</i>-Hydroxybenzaldehyde Derivatives

Properties of hydrogen bonds can induce changes in geometric or electronic structure parameters in the vicinity of the bridge. Here, we focused primarily on the influence of intramolecular H-bonding on the molecular properties in selected <i>ortho</i>-hydroxybenzaldehydes, with additional restricted insight into substituent effects. Static models were obtained in the framework of density functional theory at B3LYP/6-311+G(d,p) level. The electronic structure parameters evolution was analyzed on the basis of Atoms In Molecules (AIM) and Natural Bond Orbitals methods. The aromaticity changes related to the variable proton position and presence of substituents were studied using Harmonic Oscillator Model of Aromaticity (HOMA), Nucleus-Independent Chemical Shift (NICS) and AIM-based parameter of Matta and Hernández-Trujillo. Finally, Car–Parrinello molecular dynamics was applied to study variability of the hydrogen bridge dynamics. The interplay between effects of the substitution and variable position of the bridged proton was discussed. It was found that the hydrogen bond energies are ca. 9–10 kcal/mol, and the bridged proton exhibits some degree of penetration into the acceptor region. The covalent character of the studied hydrogen bond was most observable when the bridged proton reached the middle position between the donor and acceptor regions. The aromaticity indexes showed that the aromaticity of the central phenyl ring is strongly dependent on the bridged proton position. Correlations between these parameters were found and discussed. In the applied time-scale, the analysis of time evolution of geometric parameters showed that the resonance strengthening does not play a crucial role in the studied compounds

Influence of Environmental Humidity on Organization and Molecular Dynamics of Heteromacrocyclic Assemblies

1D and 2D NMR study, Car–Parrinello molecular dynamics, as well as classical molecular dynamics were employed to investigate <i>three derivatives of</i> benzodiazacoronands (achiral compounds which are able to form single crystals with a planar chirality) with intention to explain all subtle effects important during their preorganization, the step anticipating formation of crystals. The experimental study was carried out in two solvents: chloroform and DMSO either containing traces of water (commercial samples) or carefully dried over molecular sieves. Both methods revealed that environmental humidity has a dramatic influence on topology of solute–solvent interactions. Damping of the macrocycle dynamics by its diverse types of interactions with water molecules was shown by computational means. In the most spectacular experiment, we have proved that in chloroform-<i>d</i> during the low temperature measurements traces of water dramatically change the spectral pattern, leading to isochronous NMR signals of the AB spin system of benzodiazacoronand. The temperature of isochronous point (TIP) strongly depends on the benzodiazacoronand/water (BW) ratio. This observation opens a pathway to a new strategy based on variable temperature crystallizations and fitting of BW ratio with hope to optimize conditions for formation of chiral crystals