Theoretical characterization and biological activity investigation of indirubins, cyclin dependent kinases inhibitors

Up to now, significant research efforts have been directed towards investigating indirubin and its derivatives as potential candidates for developing new compounds with multiple biological activities. In the present work, natural indirubin and numerous of its chemical derivatives referred to as indirubins have been investigated computationally using DFT method with the B3LYP/6-311 + G(d,p) level of theory, in order to reveal structure- biological activity relationship. We started with a structural properties description. Results analysis indicated that extra interaction sites were provided through the set of substitutions in compounds (1): Indirubin-3'-monoxime, (2): Indirubin-5-sulfonic acid, (3): 5-Nitro-indirubinoxime, (4): 5'-OH-5-nitro-indirubinoxime (AGM130), (5): 7-Bromo-5'-carboxyindirubin-3'-oxime, and (6): 7 BIO and consequently, extra hydrogen bonds may be formed with the active sites of molecular targets, such as GSK-3, CDKs, and Aurora kinases, as well as the aryl hydrocarbon receptor. Subsequently, to get more information on the electronic properties of indirubin and its analogues, HOMO, LUMO, Egap, and further electronic parameters were carried out. The indirubin derivatives showed an easier interaction with its environment than indirubin, the parent compound. The UV-Visible spectra of indirubin and compounds 1-6 were also produced using TD-DFT with B3LYP functional and 6-311 + G(2d,p) basis set. The relationship between absorption and chemical structure is discussed. Two phototoxic brominated compounds showed important absorption spectra modifications. It was also found that the main absorption bands of all compounds derived from π→π*(HOMO→LUMO) transitions.Communicated by Ramaswamy H. Sarma.

Rationalizing Aggregate Structures with Orbital Contributions to the Exchange-Repulsion Energy

It is shown that repulsive interactions have a crucial influence on the structure of prototypical non-covalently bonded systems. To explain this, we propose a molecular orbital-based model for the exchange-repulsion contribution to the total interaction energy. As a central result, our model shows that energetically preferred aggregate structures frequently exhibit reduced exchange repulsion, which can be deduced from the nodal structure of certain occupied orbitals. This is used to explain key features of the intermolecular potentials of the Cl₂ -He, benzene-benzene, and benzene-hexafluorobenzene aggregates, which are not correctly reproduced by commonly applied electrostatic models.

Theoretical Study on Non-Linear Optics Properties of Polycyclic Aromatic Hydrocarbons and the Effect of Their Intercalation with Carbon Nanotubes

Results of a theoretical study devoted to comparing NLO (non-linear optics) responses of derivatives of tetracene, isochrysene, and pyrene are reported. The static hyperpolarizability β, the dipole moment μ, the HOMO and LUMO orbitals, and their energy gap were calculated using the CAM-B3LYP density functional combined with the cc-pVDZ basis set. The para-disubstituted NO₂-tetracene-N(CH₃)₂ has the highest NLO response, which is related to a large intramolecular charge transfer. Adding vinyl groups to the para-disubstituted NO₂-tetracene-N(CH₃)₂ results in an increase in the NLO responses. We further investigated the effect of the intercalation of various push-pull molecules inside an armchair single-walled carbon nanotube. The intercalation leads to increased NLO responses, something that depends critically on the position of the guest molecule and/or on functionalization of the nanotube by donor and attractor groups.

DFT evaluation of structural, electronic and variation properties for complex carbohydrates with biological interest

The synthetic bicyclic bis(hemiacetals) compounds 1,5-pyranose-9,7-pyranoses, with a structural analogy to the bicyclic monosaccharide Bradyrhizose, have been described here based on a theoretical approach, using DFT calculations with the B3LYP functional combined with the 6-311 + G(d,p) basis set. First, we have performed a geometrical and electronic properties description of (1 R,9S), (1S,9S) and (1S,9R)-1,5-pyranose-9,7-pyranoses. Results analysis indicated that, slight differences in the three-dimensional orientations of their atoms lead to an enormous difference in chemical reactivity. Consequently, (1S,9S) and (1S,9R) isomers are predicted to be the most resembling the natural bradyrhizose in structural features. To enhance the performance of these two isomers, a set of modifications through functional groups attached to the reactive sites were determined by local reactivity descriptors. Subsequently, in order to get more information on the obtained derivatives for both isomers, HOMO, LUMO, Egap and four electronic parameters were calculated and compared. The substituted systems show a good performance in chemical reactivity than the unmodified parent compounds.Communicated by Ramaswamy H. Sarma.

Performance of Hybrid DFT Compared to MP2 Methods in Calculating Nonlinear Optical Properties of Divinylpyrene Derivative Molecules

A series of divinyl-pyrene derivatives of the form D-vinyl-pyrene-vinyl-A, in which D corresponds to an electron donor group and A to an electron acceptor group, were studied in this work. The first purpose was to determine the optimal HF % exchange as incorporated in a range of hybrid functionals (M06HF, M062X, M06L, CAM-B3LYP, PBE0, BMK, and B3LYP) capable to produce, reliably and as close as possible to those obtained from MP2 calculations, NLO parameters and, in particular, first-order static hyperpolarizabilities. The CAM-B3LYP functional was revealed to be the most suitable one. The pair N(CH₃)₂/NO₂ was then determined as the most efficient pair of groups in producing appreciable NLO responses. The effect of the substitution position on the pyrene moiety was also investigated, whereby aligning the two substituents involving the D and A groups in the direction of the dipole moment as in the (1,6 DVP) derivatives was shown to be most favorable for increasing the NLO parameters.

Spectral Properties of α and β L Rhamno-Indigo Molecules and Activities Prediction Through NBO Analysis. A DFT Study

Structural and physical properties such as some spectral features of α-L rhamno-indigo and β-L rhamno-indigo molecules are presented in this paper. Results are compared with those of 5,5'-dichloro-indigo N-β-glycosidic 4-amino-4,6-didesoxyglucose (Akashine A) that exhibits a strong inhibitory activity against various human tumor cell lines. Density functional theory (DFT) using B3LYP functional and 6-31G+(d,p), 6-311+G(2d,p) and cc-pvdz as basis sets was applied to perform these studies. Calculations were carried out both in gas phase and with DMSO as an implicit solvent. Gauge including atomic orbitals (GIAO) approach was used to calculate 1H NMR chemical shifts and Time dependent density functional theory (TD-DFT) calculations were performed to determine the electronic transitions and their nature within the molecules. Moreover, stabilization energies of intra and intermolecular interactions were determined using NBO analyses. Local reactivity descriptors were computed to give insight in the nature of reactive sites. Overall, it has been shown that the nature of the glycosidic linkages has a significant influence on the molecular properties.

Vibrational normal modes calculation in the crystalline state of methylated monosaccharides: Anomers of the methyl-D-glucopyranoside and methyl-D-xylopyranoside molecules

A structural investigation of the organic molecules is being carried out using vibrational spectroscopy. In this study, normal co-ordinate calculations of anomers of the methyl-D-glucopyranoside and methyl-β-D-xylopyranoside in the crystalline state have been performed using the modified Urey-Bradley-Shimanouchi force field (mUBSFF) combined with an intermolecular potential energy function. The latter includes Van der Waals interactions, electrostatic terms, and explicit hydrogen bond functions. The vibrational spectra of the compounds recorded in the crystalline state, in the 4000-500 cm(-1) spectral region for the IR spectra, and in the 4000-20 cm(-1) spectral range for the Raman spectra are presented. After their careful examination, several differences in the intensities and frequency shifts have been observed. The theoretical spectra have been obtained after a tedious refinement of the force constants. Thus, on the basis of the obtained potential distribution, each observed band in IR and in Raman has been assigned to a vibrational mode. The obtained results are indeed in agreement with those observed experimentally and thus confirm the previous assignments made for the methyl-α and β-D-glucopyranoside, as well as for the methyl-β-D-xylopyranoside.

Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water

We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.

Relaxed energetic maps of kappa-carrabiose: a DFT study

The B3LYP density function was used with the 6-31G(d) basis set to perform relaxed energetic contour maps of the charged form of kappa-carrabiose in the gas phase and for the neutral form first in the gas phase and then by simulating the presence of water as solvent using the Onsager model. Only one starting conformation has been considered to perform all the calculations. Rigid energetic maps have been then constructed either by addition of diffuse or polarization functions to the basis set obtaining in that way 6-31+G(d)//6-31G(d), 6-31+G(d,p)//6-31G(d), and 6-311++G(d,p)//6-31G(d) energetic maps that have been carefully examined. The obtained structures corresponding to the lower energy conformers have been then fully optimized using different basis sets with the B3LYP method, a reversion in term of energy has been observed for the two first minima in the case of the charged disaccharide in the gas phase, this was attributed to the large grid of 30 degrees that could lead to the exclusion of an intermediate value corresponding to the real minimum of energy. We thus suggest that after establishing potential energy maps it is essential to proceed to full optimizations of the lower energy conformers. Calculations using the more accurate correlated method MP2 with the 6-31G(d) basis set have also been performed for conformers of the two disaccharides in the gas phase.

Normal coordinates analyses of disaccharides constituted by D-glucose, D-galactose and D-fructose units

A thorough study of the vibrational spectra of two disaccharides, melibiose and turanose, is presented in this work. The infrared and Raman spectra of these two compounds have been first recorded in the mid infrared range then in the far infrared region (for Raman only). These spectra constitute the main experimental support for the calculations of the modified Urey-Bradley-Shimanouchi force fields of these two disaccharides. Good agreements have been obtained between the observed and calculated frequencies. In a second time, spectra of O-deuterated derivatives have been recorded and used in order to confirm some of the frequency assignments and to test the validity of the obtained force fields.

Normal coordinates analyses of beta-D-allose and alpha-D-talose in the crystalline state

IR and Raman spectra of beta-d-allose, alpha-d-talose and beta-d-allose O-D(5) have been recorded in the 4000-400 cm(-1) and in the 4000-20 cm(-1) regions. These spectra constitute the experimental support that allows to reproduce theoretically the vibrational frequencies and to establish a force field for these saccharides through a normal coordinate analysis. For this purpose, a modified UBSFF has been combined with an intermolecular potential energy function that includes the Van der Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The initial force field parameters are derived either from those of D-glucose or D-galactose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The obtained results reproduce the experimental frequencies and in order to test the validity of the obtained force field, it has been applied to beta-D-allose O-D(5).

Harmonic dynamics of alpha- and beta-methyl-D-galactopyranoside in the crystalline state

The study of the anomeric differences observed on the spectra of methyl-alpha- and methyl-beta-D-galactopyranoside is the essential goal of this investigation. Thus, after a careful examination of the IR and Raman spectra of these two compounds, several differences in the intensities and frequency shifts are observed. This is especially noted in the region 1000-700 cm(-1). In order to make some assignments with more precision, the normal modes analyses of the two compounds are performed in the crystalline state. For this purpose, a modified Urey-Bradley-Shimanouchi force field has been combined with an intermolecular potential energy function. The initial set of force constants comes from those of alpha- and beta-D-galactopyranosyl, then the force constants have been varied, so as to obtain a good agreement between the observed and the calculated vibrational frequencies. The obtained results have finally reproduced the experimental data and have confirmed the previous assignments made for the methyl-alpha- and methyl-beta-D-galactopyranoside. The calculations have demonstrated also the transferability of the set of parameters of the initial force field of D-galactose to methyl-D-galactopyranoside.

Harmonic dynamics of beta-D-fructopyranose

The vibrational spectra of beta-D-fructopyranose crystals have been recorded in the 4000-400 cm(-1) region using the infrared and in the 4000-20 cm(-1) region using the Raman. These spectra are used as an experimental basis in order to establish a force field for the beta-D-fructopyranose molecule in the crystalline state through a normal co-ordinates analysis. For this purpose, a modified Urey-Bradley-Shimanoushi force field was combined with an intermolecular potential energy function that includes the van-der-Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The force field parameters are derived from those of beta-D-glucose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The results obtained demonstrate the reliability and the transferability of the set of parameters constituting the initial force field. The fitted force field reproduces the experimental spectra to a marked degree of accuracy.