Co2+ binding cysteine and selenocysteine: a DFT study

In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species. In particular, we have focused our attention on the role of sulfur and selenium in the metal binding process and on the resulting deprotonation of the thiol and seleniol functions. From the present calculations we are able to explain, both from electronic structure and thermochemical point of views, a metal-induced thiol deprotonation as observed in gas-phase experiments. A similar process is expected in the case of selenocysteine. In fact, cobalt was found to have a preferential affinity with respect to thiolate and selenolate functions. This can be related to the observation that only S and Se are able-in thiolate and selenolate states-to make a partial charge transfer to the cobalt thus forming very stable complexes. Globally, very similar results are found when substituting S with Se, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets.     

Conformal prediction of HDAC inhibitors

The growing interest in epigenetic probes and drug discovery, as revealed by several epigenetic drugs in clinical use or in the lineup of the drug development pipeline, is boosting the generation of screening data. In order to maximize the use of structure–activity relationships there is a clear need to develop robust and accurate models to understand the underlying structure–activity relationship. Similarly, accurate models should be able to guide the rational screening of compound libraries. Herein we introduce a novel approach for epigenetic quantitative structure–activity relationship (QSAR) modelling using conformal prediction. As a case study, we discuss the development of models for 11 sets of inhibitors of histone deacetylases (HDACs), which are one of the major epigenetic target families that have been screened. It was found that all derived models, for every HDAC endpoint and all three significance levels, are valid with respect to predictions for the external test sets as well as the internal validation of the corresponding training sets. Furthermore, the efficiencies for the predictions are above 80% for most data sets and above 90% for four data sets at different significant levels. The findings of this work encourage prospective applications of conformal prediction for other epigenetic target data sets.     

Microsolvation of glycine: a DFT study

PBE1PBE/6-311+G(d,p) computations exploring the microsolvation of neutral and zwitterionic glycine are reported. A broad configuration search was performed to identify the lowest energy clusters of glycine with one to seven water molecules. The structures of the clusters are analyzed on the basis of the hydrogen-bonding network established between the water molecules and between water and glycine. Neutral glycine is favored when associated with zero to six water molecules, but with seven water molecules the two structures are isoenergetic.     

Effect of GTP and GDP nucleotides on vinblastine binding affinity to tubulin: a DFT study

Vinblastine (VLB) is an anticancer agent that inhibits microtubule assembly by binding with tubulin. Density functional theory (DFT) calculations are used to examine low-energy minima of the energy surface of vinblastine-tubulin complex. Thermodynamic data of the binding site of vinblastine to tubulin are extracted with the hybrid DFT (B3LYP (Becke, three-parameter, Lee–Yang–Parr)) method, and then the influence of several solvents, such as water, methanol and ethanol, and different temperatures are discussed on infrared parameters by self-consistent reaction field (SCRF = dipole) method. The effect of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) nucleotides on vinblastine binding affinity to tubulin was realised in water solvent by comparing the changes of ?G (Gibbs free energy) of VLB-tubulin and VLB-tubulin bonded to GTP or GDP. The result showed that GDP and GTP increase significantly the binding affinity and the role of GDP is more important than that of GTP.     

DFT study of structure and binding energies of Fe-corannulene complex

Density functional theory (DFT) based theoretical calculations are performed to identify the ground-state geometries, the spin multiplicities, and the relevant energetics of neutral and positively charged Fe-corannulene complexes. Our calculations show that the on-top site of the six-membered ring (eta(6)) of corannulene molecule is the most preferred binding site for both Fe atom and Fe(+) ion. The electrostatic potential (ESP) surface picture is employed to explain the preference of the eta(6)- over the eta(5)-binding site (on-top site of central pentagon) of corannulene. Though in both neutral and cationic species the eta(6)-site is the most preferred binding site, the ground-state geometries of these complexes are different. The Fe(+) cation prefers to bind to the convex face of the corannulene, whereas the neutral Fe atom prefers slightly the concave to the convex face. The ionization-induced structural changes are reflected in the large energy difference between the vertical and adiabatic ionization potential values. We also show that the dissociation of Fe(+)-corannulene complex to corannulene + Fe(+) is just as likely as that to Fe + (corannulene)(+).     

Elucidating the mechanism of binding of chromate to cucurbit[6]uril: a DFT study

We report the binding of chromate, a toxic heavy metal ion to the macrocyclic host molecule, cucurbituril using density functional theory. Due to the anionic nature of the guest molecule and the portals of the host molecule, we propose that the binding mechanism should be assisted by cations. The calculated barrier for chromate binding to cucurbituril is found to be?~17?kcal?mol^?1. The large barrier can be attributed to portal opening of the host molecule, electrostatic repulsion between the guest molecule and the portals of the host molecule and the solvent re-organization around guest molecule.     

Polar bromination of cyclopropane: a DFT study

Hitherto the polar addition of bromine to cyclopropane has been considered as a two-step process. Current calculations have established the energetics for the proposed cation-anion pairs required by these mechanisms. An energetically lower pathway is proposed here in the form of a syn-cycloaddition process. Compared to the two-step process, a significantly lower activation enthalpy for this process has been found. The stereochemical consequences of the cyclic mechanism are retention-retention for the two adding moieties. This result is consistent with published experimental data on the bromination of a deuterated cyclpropane.     

Diastereoselectivity in lewis-Acid-catalyzed mukaiyama aldol reactions: a DFT study

The basis for diastereoselectivity in Lewis-acid-catalyzed Mukaiyama aldol reactions was studied using density functional theory. By exploring the conformations of the transition structures for the diastereodifferentiating step of seven different reactions, simple models were generated. The effects of varying the substituents on the enol carbon and the α-carbon of the silyl enol ether from methyl to tert-butyl groups and the substituent on the aldehyde from methyl to phenyl groups were investigated by comparison of the transition structures for different reactions. Expanding on the previous qualitative models by Heathcock and Denmark, we found that while the pro-anti pathways take place via antiperiplanar transition structures, the pro-syn pathways prefer synclinal transition structures. The relative steric effects of the Lewis acid and trimethyl silyl groups and the influence of E/Z isomerism on the aldol transition state were investigated. By calculating 36 transition structures at the M06/6-311G*//B3LYP/6-31G* level of theory and employing the IEFPCM polarizable continuum model for solvation effects, this study expands the mechanistic knowledge and provides a model for understanding the diastereoselectivity in Lewis-acid-catalyzed Mukaiyama aldol reactions.     

Oxoanion binding by guanidiniocarbonylpyrrole cations in water: a combined DFT and MD investigation

Structures and properties of nonbonding interactions involving guanidinium-functionalized hosts and carboxylate substrates were investigated by a combination of ab initio and molecular dynamics approaches. The systems under study are on one hand intended to be a model of the arginine-anion bond, so often observed in proteins and nucleic acids, and on the other to provide an opportunity to investigate the influence of molecular structure on the formation of supramolecular complexes in detail. Use of DFT calculations, including extended basis sets and implicit water treatment, allowed us to determine minimum-energy structures and binding enthalpies that compared well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions through three hydrogen bonds, one of which is bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting of a rotation of about 180 degrees around the guanidiniocarbonylpyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed in the presence of explicit water molecules by use of the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM-PBSA) and linear interaction energy (LIE) approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes cannot be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible for several low-energy metastable structures.     

Reactions of aldehyde with collagen: a DFT study

Structural Chemistry - The reaction mechanisms of several amino acids (Asn, Gln, Arg, His, and Lys) in the collagen with aldehyde were studied using density functional theory method. Based on the...     

Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

ABSTRACT

In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), N-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.     

A DFT study of a novel oxime anticancer trans platinum complex: Monofunctional and bifunctional binding to purine bases

The first and second substitution reactions binding of the anticancer drug trans‐[Pt((CH₃)₂C?NOH)((CH₃)₂CHNH₂)Cl₂] to purine bases were studied computationally using a combination of density functional theory and isoelectric focusing polarized continuum model approach. Our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate either trans‐ or cis‐monoadducts via identical or very similar trans trigonal‐bipyramidal transition‐state structures. Furthermore, these monoadducts can subsequently close by coordination to the adjacent purine bases to form 1,2‐intrastrand Pt‐DNA adducts and eventually distort DNA in the same way as cisplatin. Thus, it is likely that the transplatin analogues have the same mechanism of anticancer activity as cisplatin. For the first substitutions, the activation free energies of monoaqua complexes are always lower than that of diaqua complexes. The lowest activation energy for monoaqua substitutions is 16.2 kcal/mol for guanine and 16.5 kcal/mol for adenine, whereas the lowest activation energy for diaqua substitutions is 17.1 kcal/mol for guanine and 25.9 kcal/mol for adenine. For the second substitutions, the lowest activation energy from trans‐monoadduct to trans‐diadduct is 19.1 kcal/mol for GG adduct and 20.7 kcal/mol for GA adduct, whereas the lowest activation energy from cis‐monoadduct to cis‐diadduct is 18.9 kcal/mol for GG adduct and 18.5 kcal/mol for GA adduct. In addition, the first and second substitutions prefer guanine over adenine, which is explained by the remarkable larger complexation energy for the initial RC in combination with lower activation energy for the guanine substitution. Overall, the hydrogen‐bonds play an important role in stabilizing these species of the first and second substitutions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Core excitations in MgO: a DFT study with cluster models

The time dependent density functional theory has been employed to calculate the absorption spectra relative to core excitation of Mg 1s, Mg 2p and O 1s orbitals of solid MgO. Cluster models of various size and shape are considered, embedded within an array of point charges to simulate the Madelung potential. Comparison with experimental data and previous theoretical calculations allows a precise assessment of the performances of the present method, which is competitive and promising for further application to more complex systems, like transition metal oxides.     

卟啉-富勒烯体系光激发电子转移的理论研究

在分子水平研究新型人工光俘获材料对于太阳能电池的发展具有重要意义。本文采用TD-DFT方法研究了卟啉-富勒烯(P-C60)体系的光诱导电子转移过程。该过程由三个过程组成:(1)光激发过程,P-C60由基态激发至卟啉局域激发(LE)态;(2)电荷分离(CS)过程形成卟啉至富勒烯的电荷转移(CT)态;(3)电荷重组(CR)过程,CT态返回到基态。我们通过分析分子轨道指认了LE态和CT,并获得了这两个激发态的结构。采用广义Mulliken-Hush(GMH)方法计算体系电荷分离和电荷重组过程的态态间电子耦合,和实验测量的电子转移速率获得定性一致的结果。本工作为分析、预测光诱导电荷转移过程提供了有效的手段。     

Reactivity of metaphosphate and thiometaphosphate in water: a DFT study

Metaphosphate is known to be highly reactive to water, whereas thiometaphosphate is relatively stable in aqueous solution. The difference in their reactivity has important mechanistic implications in interpreting the "thio effect" in phosphoryl transfer reactions. In this work, density functional theory is used to investigate the reactivity of both metaphosphate and its thio-substitute in their complexes with one, two, and three waters, and in aqueous solution. Barrier heights for converting metaphosphate to orthophosphate have been determined by geometry optimization. The results confirm that metaphosphate is consistently more reactive than thiometaphosphate and the activation free energy for both species decreases with the number of water molecules. The relative stability of thiometaphosphate is attributed to its less positively charged phosphorus atom.     

Adsorption and diffusion on a phosphorene monolayer: a DFT study

A computational study of the adsorption and diffusion behavior of alkali and alkaline earth metal atoms on a phosphorene monolayer is reported. Our calculations were performed within the framework of density functional theory using the Perdew–Burke–Ernzerhof functional and projector augmented wave potentials, as derived from the generalized gradient approximation. Our binding energy calculations for various potential adsorption sites showed that the site located above the center of a triangle formed by three surface phosphorus atoms is the most attractive to all adatoms. In addition, simulation of the diffusion of adatoms across the surface of the phosphorene monolayer showed that the diffusion is anisotropic, with K having the lowest diffusion barrier (0.02 eV along the zigzag pathway). To the best of our knowledge, this is the lowest diffusion barrier of any metal adatom on a single layer of phosphorene. While phosphorene exhibited significantly better adatom adsorption and diffusion than graphene, it also showed a reduced storage capacity compared to graphene, most probably due to the structural distortion induced by the oversaturated phosphorene surface. This finding strongly suggests that a phosphorene–graphene hybrid system could be employed as a promising high-capacity ion anode.     

Synthesis of 2-quinolinecarboxamide derivatives as potential HDAC inhibitors

Inhibition of histone deacetylase activity appears as an original and effective approach for the treatment of cancer. A series of novel quinoline-containing derivatives has been synthesized and found that some of these compounds possess nanomolar histone deacetylase inhibitory activity.     

Allenediazonium ions and their protonation chemistry: a DFT study

The parent allenediazonium monocation H2C[double bond]C[double bond]CH(N2+) and ten of its substituted derivatives XYC[double bond]C[double bond]C(Z)N2+ (with F, CF3, Me, OMe, and Me2N as substituents) were studied by DFT at the B3LYP/6-31++G** level. Except for the Me2N-substituted derivative that forms a monocation-N2 complex, structurally intact allenediazonium ions were obtained as minima in all cases. Protonation studies at various sites were performed on allenediazonium cations, and relative energies of the resulting minima were used to identify the energetically most favored dications. In the majority of cases, protonation at the central carbon of the allenic moiety (C2) is most favored, forming delocalized allyl cation-N2+ species. The same dication structure is formed via initial C3-protonation, followed by a formal hydride shift, in cases where a carbocation-stabilizing group is placed at C3. When a CF3 group is placed at C3, initial protonation at C1 resulted in a 1,3-fluorine shift, to generate a fluoroallyl cation linked to a CH2N2+ moiety. Structural features in the allenediazonium monocations and their protonated dications were examined, taking into account their geometrical features, computed charges, and the GIAO NMR shifts.