Density functional computations of enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes

The enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes was studied by means of the density functional theory (DFT). All the structures were optimized completely at the B3LYP/6-31G(d,p) level. To obtain more exact energies, single-point energy calculations at B3LYP/6-31+G(d,p) level were carried out on the B3LYP/6-31G(d,p) geometries. As shown, this enantioselective alkynylation was endothermic. The chirality-determining step for the alkynylation was the formation of the catalyst–ethanol complexes and the transition states for this step involved a six-membered ring. The dominant products predicted theoretically were of (R)-chirality, in good agreement with experiment.      

Computational molecular characterization of the flavonoid Morin and its Pt(II), Pd(II) and Zn(II) complexes

In this work, we make use of a model chemistry within density functional theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Morin and its Pt(II), Pd(II) and Zn(II) complexes, as well to predict their IR and UV-Vis spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for these molecules.     

Bile acid structure-activity relationship: evaluation of bile acid lipophilicity using 1-octanol/water partition coefficient and reverse phase HPLC

Two independent methods have been developed and compared to determine the lipophilicity of a representative series of naturally occurring bile acids (BA) in relation to their structure. The BA included cholic acid (CA), chenodeoxycholic acid (CDCA), ursodeoxycholic acid (UDCA), deoxycholic acid (DCA), hyodeoxycholic acid (HDCA), ursocholic acid (UCA), hyocholic acid (HCA), as well as their glycine and taurine amidates. Lipophilicity was determined using a 1-octanol/water shake-flask procedure and the experiments were performed at different pH and ionic strengths and at initial BA concentrations below their critical micellar concentrations (CMC) and the water solubility of the protonated form. The experimental data show that both the protonated (HA) and ionized (A-) forms of BA can distribute in 1-octanol, and consequently a partition coefficient for HA (logP' HA) and for A- (logP' A-) must be defined. An equation to predict a weighted apparent distribution coefficient (D) value as a function of pH and pKa has been developed and fits well with the experimental data. Differences between logP for protonated and ionized species for unconjugated BA were in the order of 1 log unit, which increased to 2 for glycine-amidate BA. The partition coefficient of the A- form increased with Na+ concentration and total ionic strength, suggesting an ion-pair mechanism for its partition into 1-octanol. Lipophilicity was also assessed using reverse phase chromatography (C-18-HPLC), and a capacity factor (K') for ionized species was determined. Despite a broad correlation with the logP data, some BA behaved differently. The logP values showed that the order of lipophilicity was DCA greater than CDCA greater than UDCA greater than HDCA greater than HCA greater than CA greater than UCA for both the protonated and ionized unconjugated and glycine-amidate BA, while the K' data showed an inversion for some BA, i.e., DCA greater than CDCA greater than CA greater than HCA greater than UDCA greater than HDCA greater than UCA. The logP data fitted well with other indirect measurements of BA monomeric lipophilicity such as albumin binding or accessible total hydrophobic surface area data calculated by energy minimization and molecular computer graphics. Differences between unconjugated and amidated BA are consistent with the presence of an amide bond and a lower pKa when pH dependence was studied. Capacity factors, on the other hand, were related to properties of BA micelles such as cholesterol-solubilizing capacity and membrane disruption, reflecting the BA detergency.(ABSTRACT TRUNCATED AT 400 WORDS)     

Molecular and statistical modeling of reduction peak potential and lipophilicity of platinum(IV) complexes

We report the results of the quantitative structure–property relationship analysis of 31 Pt(IV) complexes, for three of which the synthesis is reported for the first time. The X-ray structural analysis of one complex of the series was performed to demonstrate that the PM6 semiempirical method satisfactorily reproduces key features of the geometry of the complexes investigated. Molecular properties extracted from such calculations were then used to construct models of experimental data such as electrochemical peak potentials (evaluated by cyclic voltammetry) and the octanol–water partition coefficient (evaluated by a reversed-phase high performance liquid chromatography method), which are key aspects in the design of such Pt(IV) complexes as potential anticancer prodrugs. Statistically accurate models for both properties were found using combinations of surface areas, orbital energies, dipole moments, and atomic partial charges. These models could form the basis of virtual screening of potential drug molecules, allowing the prediction of properties, closely related to the antiproliferative activity of Pt(IV) complexes, directly from calculated data.     

The platinum complexes with histamine: Pt(II)(Hist)Cl2, Pt(II)(Iodo-Hist)Cl2 and Pt(IV)(Hist)2Cl2

The Pt(II) and Pt(IV) complexes with histamine were calculated by using more than 20 DFT functionals and various basis sets. Based on the comparison between the X-ray and theoretical geometrical parameters of the Pt(II)(Hist)Cl₂ complex the MPW1PW91, OPW91 and SVWN5 functionals combined with the 6-311G^∗∗ basis set for non-metallic and SDD (ECP) basis set for platinum were found to yield the most satisfactory agreement. The structure of the Pt(II) complex with iodohistamine important for pharmacy, so far isolated only in minute amounts, was predicted by using the MPW1PW91 functional. Comparison of the theoretical NMR chemical shifts of the Pt(II)(Hist)Cl₂ complex with those found experimentally have shown that the theoretical ¹H and ¹³C NMR chemical shifts are in plausible agreement with the experimental ones, whereas the theoretical ¹⁹⁵Pt chemical shifts fit the experimental values only when the relativistic approach is applied within the ZORA formalism. We confirmed suitability of the three selected functionals for reproduction of the experimental structure of Pt complexes at fourth oxidation state by using the cis- and ions as models. Finally, with the selected theoretical methods, the structures and stabilities of four Pt(IV)(Hist)₂Cl₂ complex isomers were predicted.     

The prediction of human acute systemic toxicity by the EDIT/MEIC in vitro test battery: the importance of protein binding and of partitioning into lipids

The aim of the two studies presented in this paper was to further improve the predictability of the original Multicentre Evaluation of In Vitro Cytotoxicity (MEIC) in vitro test battery for acute systemic toxicity. In the first study, whether a protein-free cytotoxicity assay could improve the prediction of human acute systemic toxicity was investigated. The cytotoxicity of 39 MEIC reference chemicals was measured by the neutral red uptake inhibition test after 30 minutes in phosphate-buffered saline (PBS), with hepatoma-derived Fa32 cells. The results were compared with the corresponding values obtained in complete culture medium, including 10% fetal calf serum. Mercuric chloride and hexachlorophene were much more cytotoxic in PBS, as was the case, to a lesser extent, for seven other chemicals. Potassium cyanide and eight other chemicals were less cytotoxic in PBS than in complete culture medium, probably because of poor physiological conditions. The correlation between the cytotoxicity measured in PBS and human acute toxicity was rather low, but became of the same order as for other assays, when mercuric chloride and hexachlorophene were withdrawn from the comparison. In the second study, modelling of human lethal blood concentrations by using the results of the three cell line tests of the original MEIC test battery were complemented by logP (octanol-water partition coefficient) values. The introduction of logP into the modelling did not improve the correlations, but some improvement of both R(2) and Q(2) was obtained by expanding the logP values with logP(2) values. The highest R(2) (0.84) and Q(2) (0.80) values were obtained for a model in which both experimental and calculated (ambiguous) logP values were used. When only experimental logP values were used, the corresponding values were 0.80 and 0.78. These two studies showed that including protein binding and the partition of chemicals in the MEIC in vitro test battery is important, in order to improve the predictability of the results obtained.     

Cytotoxic effect, differentiation, inhibition of growth and theoretical calculations of an N,N-donor ligands and its platinum(II), palladium(II) and copper(II) complexes

The new pyrazole ligand 5-(2-hydroxyphenyl)-3-methyl-1-(2-pyridylo)-1H-pyrazole-4-carboxylic acid methyl ester (2) and the corresponding Pt(II), Pd(II) and Cu(II) complexes 3-5 have been synthesized as potential anticancer compounds, and characterized using IR, and (1)H NMR as well as mass spectrometry. The 3-D structures of the Cu(II) complexes were determined by quantum mechanic calculation DFT methodology (density functional theory). The cytotoxicity assay of the ligand and complexes has been performed on leukemia cell lines. In general, the complexes showed lower cytotoxicity than cisplatin, and the Pt(II) and Cu(II) complexes were found to be more efficient in the induction of leukemia cell death than the Pd(II) complex. Our investigations indicate that the antiproliferating activity of the Pt(II) and Cu(II) complexes was partly due to the modulation of cellular differentiation.     

Uptake of antitumor platinum(II)-complexes by cancer cells, assayed by inductively coupled plasma mass spectrometry (ICP-MS)

A systematic study on intracellular Pt uptake and Pt accumulation ratio in breast cancer MCF-7 cell line has been performed on a number of Pt(II)-complexes, namely cisplatin, carboplatin and oxaliplatin, clinically employed as antitumor drugs, trans- and cis-[Pt(Cl)2(pyridine)2] and cis-[Pt(Cl)2(pyridine)(5-SO3H-isoquinoline)] complexes, previously investigated also as potential telomerase inhibitors. In particular, long incubation times have been chosen in order to understand the fate of the complexes in the cells. For this purpose, sub-acute drug concentrations must be employed and, therefore, a very sensitive method of analysis like as inductively coupled plasma mass spectrometry (ICP-MS) superior to the widely employed atomic absorption spectroscopy (AAS) has been adopted. Any relationships among uptake/accumulation and several parameters such as drug structure, lipophilicity, drug concentration and incubation time have been sought and analyzed: the bulk of data point for a passive diffusion mechanism through the cell membrane.     

离体鼠肝细胞及P-450酶系与拟除虫菊酯类杀虫剂的相互作用

经研究表明顺式氯氰菊酯、甲氰菊酯、氟氰菊酯、氰戊菊酯在正辛醇——水相中的分配系数(logP)分别为6.13,5.50,5.55和4.02。离体培养的大白鼠原代肝细胞对上述杀虫剂(除氟氰菊酯外)的吸收系数(q值)分别为322.6,281.1,201.9。上述杀虫剂在离体培养的原代肝细胞中降解很快,温育30分钟后降解速率分别为90.0％(顺式氯氰菊酯)、86.2％(甲氰菊酯)、69.5％(氰戊菊酯)。同时有明显的减少离体培养的鼠肝细胞中P-450含量的作用,其中以溴氰菊酯和顺式氯氰菊酯作用较明显。在溴氰菊酯处理组中,随杀虫剂浓度的升高,这种减少P-450含量的作用明显增强。检查温育反应90分种后的细胞悬浮反应液,对照组仍维持高的细胞存活率(74.4％和91.2％),而杀虫剂处理组,除甲氰菊酯处理组仍有42.4％的存活率外,其余各杀虫剂(溴氰菊酯各浓度组和顺式氯氰菊酯处理组)均未检出存活的细胞。结果表明,试验所用的几种拟除虫菊酯类杀虫剂具有一定的细胞毒性。它们在鼠肝细胞中的降解代谢可能主要不是由于多功能氧化酶起作用。另外,杀虫剂的亲脂性与q值及在肝细胞中的降解速率三者间有一定的正相关。     

Transport of steroid hormones facilitated by serum proteins.

The affinities with steroid hormones (alpha-estradiol, ethynylestradiol, progesterone, androsterone, dehydroisoandrosterone and testosterone) were observed for Cohn's fraction IV-1 and V (albumin). It was estimated from the comparison with the binding coefficient K (protein-bound form/free form of hormone) in a 3.5% (w/v) bovine serum albumin (BSA) solution that 40-80% of bound hormone in bovine serum is the BSA-bound form. It becomes clear in a liquid membrane system consisting of a hexane source phase (I), a water phase and a hexane receiving phase (II) that the transport flux of hormone is governed primarily by the partition coefficients between the water/hexane phases. In the case of a hormone with a lower partition coefficient, the uptake process from the hexane phase (I) to the water phase is a rate-determining step in the transport system and the serum proteins accelerate the transport of hormones, while with an increase in the partition coefficient the rate-determining step changes from the uptake step to the release step from the water phase to the hexane phase (II) and the hormone transport is decelerated owing to the significant decrease of free hormone concentration in the aqueous phase by the associated with serum proteins for the system having the restricted amount of hormone in the hexane source phase.     

Calculation of lipophilicity for Pt(II) complexes: experimental comparison of several methods

Platinum containing compounds are promising antitumor agents, but must enter cells before reaching their main biological target, namely DNA. Their distribution within the body, and hence their activity is to a large extent determined by their lipophilicity, thus there is a strong interest to develop computational methods to predict this important property. This study analyses accuracy of five methods, namely ALOGPS, KOWWIN, CLOGP and two quantum chemical approaches, to predict octanol/water partition coefficients (log P) for sets of 43 and 12 Pt(II) complexes, collected from the literature and measured by the authors, respectively. All methods gave generally poor results with mean absolute error (MAE) of between 0.8 and 3 log units for prediction of new compounds. Extension of the ALOGPS program with data from the literature set resulted in the best prediction ability, MAE = 0.46, for the measured molecules. The program was also able to correctly predict errors in calculated log P values. It is freely available for interactive use at http://www.vcclab.org.     

Biotransformation in double-phase systems: physiological responses of Pseudomonas putida DOT-T1E to a double phase made of aliphatic alcohols and biosynthesis of substituted catechols

Pseudomonas putida strain DOT-T1E is highly tolerant to organic solvents, with a logP(ow) (the logarithm of the partition coefficient of a solvent in a two-phase water-octanol system of > or =2.5. Solvent tolerant microorganisms can be exploited to develop double-phase (organic solvent and water) biotransformation systems in which toxic substrates or products are kept in the organic phase. We tested P. putida DOT-T1E tolerance to different aliphatic alcohols with a logP(ow) value between 2 and 4, such as decanol, nonanol, and octanol, which are potentially useful in biotransformations in double-phase systems in which compounds with a logP(ow) around 1.5 are produced. P. putida DOT-T1E responds to aliphatic alcohols as the second phase through cis-to-trans isomerization of unsaturated cis fatty acids and through efflux of these aliphatic alcohols via a series of pumps that also extrude aromatic hydrocarbons. These defense mechanisms allow P. putida DOT-T1E to survive well in the presence of high concentrations of the aliphatic alcohols, and growth with nonanol or decanol occurred at a high rate, whereas in the presence of an octanol double-phase growth was compromised. Our results support that the logP(ow) of aliphatic alcohols correlates with their toxic effects, as octanol (logP(ow) = 2.9) has more negative effects in P. putida cells than 1-nonanol (logP(ow) = 3.4) or 1-decanol (logP(ow) = 4). A P. putida DOT-T1E derivative bearing plasmid pWW0-xylE::Km transforms m-xylene (logP(ow) = 3.2) into 3-methylcatechol (logP(ow) = 1.8). The amount of 3-methylcatechol produced in an aliphatic alcohol/water bioreactor was 10- to 20-fold higher than in an aqueous medium, demonstrating the usefulness of double-phase systems for this particular biotransformation.     

Combined Density Functional Theory (DFT) and Continuum Calculations of pK(a) in Carbonic Anhydrase

Deprotonation of zinc-bound water in carbonic anhydrase II is the rate-limiting step in the catalysis of carbon dioxide between gas- and water-soluble forms. To understand the factors determining the extent of dissociation, or pK(a), of the zinc-bound water, we apply quantum chemistry calculations to the active site coupled with a continuum model of the surrounding environment. Experimentally determined changes in pK(a) associated with mutations of the active site are well reproduced by this approach. Analysis of the active site structure and charge/dipole values provides evidence that mutations cause changes in both conformation of the active site structure and local polarization, which accounts for the shifts in pK(a). More specifically, the shifts in pK(a) correlate with the dipole moments of the zinc-bound water upon deprotonation. The data further support the conclusion that the distinct pK(a) values found in mutations of the same type, but applied to different sites, result from asymmetric ligation and different electronic environments around the zinc ion.     

Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index

A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree–Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r?=?0.9216) was obtained with the AM1 Ford–Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r?=?0.9220). Nevertheless, in spite of a marginally lower performance (r?=?0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values.

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Graphical abstract The hydrophilic/lipophilic index (HLI)

     

Effect of the photocatalytic activity of TiO(2) on plasmid DNA

We investigated the photodynamic DNA strand-breaking activity of TiO(2). A solution of super-coiled pBR 322 DNA was irradiated with 5 J/cm(2) of UVA in the presence of TiO(2) and the products were analyzed by using gel electrophoresis. The ratio of open-circular DNA to super-coiled circular DNA was calculated from the resulting peak areas as a DNA strand-breaking index (SBI). The SBI of anatase-structure TiO(2) (band gap=3.23 eV) was greater than that of rutile structure (band gap=3.06 eV), and the level of SBI correlated with the photocatalytic activity for degradation of 2-propanol. The inhibitory effects of active oxygen scavengers, including DMSO, glutathione and histidine, on the DNA strand-breaking activity were examined. All of the scavengers except ascorbic acid showed inhibitory effects, as did several polyhydric alcohols including mannitol, a well-known hydroxyl radical scavenger. These results suggest that the photodynamic DNA strand-breaking activity of TiO(2) is due to active oxygen species, especially hydroxyl radicals. Polyhydric alcohols showed an inverse correlation between the inhibitory effect on DNA strand-breaking activity and the octanol/water partition coefficient (logP).     

Biological evaluations of newly-designed Pt(II) and Pd(II) complexes using spectroscopic and molecular docking approaches

To perform biological evaluations of newly-designed Pt(II) and Pd(II) complexes, the present study was conducted with targeted protein human serum albumin (HSA) and HCT116 cell line as model of human colorectal carcinoma. The binding of Pt(II) and Pd(II) complexes to HSA was analyzed using fluorescence spectroscopy and molecular docking. The thermal stability and alterations in the secondary structure of HSA in the presence of Pt(II) and Pd(II) complexes were investigated using the thermal denaturation method and circular dichroism (CD) spectroscopy. The cytotoxicity of the Pt(II) and Pd(II) complexes was studied against the HCT116 cell line using MTT assay. The binding analysis revealed that the fluorescence findings were well in agreement with docking results such that there is only one binding site for each complex on HSA. Binding constants of 8.7?×?10³ M^?1, 2.65?×?10³ M^?1, 0.3?×?10³ M^?1, and 4.4?×?10³ M^?1 were determined for Pd(II) and Pt(II) complexes (I–IV) at temperature of 25?°C, respectively. Also, binding constants of 1.9?×?10³ M^?1, 15.17?×?10³ M^?1, 1.9?×?10³ M^?1, and 13.1?×?10³ M^?1 were determined for Pd(II) and Pt(II) complexes (I–IV) at temperature of 37?°C, respectively. The results of CD and thermal denaturation showed that the molecular structure of HSA affected by interaction with Pt(II) and Pd(II) complexes is stable. Cytotoxicity studies represented the growth suppression effect of the Pt(II) and Pd(II) complexes toward the human colorectal carcinoma cell line. Therefore, the results suggest that the new designed Pt(II) and Pd(II) complexes are well promising candidates for use in cancer treatment, particularly for human colorectal cancer.

Communicated by Ramaswamy H. Sarma     

Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?

We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (α, β and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.     

Alpha-phenyl-N-tert-butyl nitrone (PBN) derivatives: synthesis and protective action against microvascular damages induced by ischemia/reperfusion

Nitrones 4-7, structurally related to PBN (1), were prepared by reaction of the corresponding aromatic aldehydes with N-tert-butyl hydroxylamine. The protective effects of these nitrones against microvascular damages in ischemia/reperfusion in the 'hamster cheek pouch' assay were studied and 1, as well as 4a, 4b, and 7 (derived from piperonal, O-benzyl vanillin, and furfural, respectively), showed to be more active than shark cartilage or alpha-tocopherol. No correlation was found between the protective effect of these nitrones and their logP (partition coefficient) or their capacity to trap (*)OH and (*)CH(3) radicals.