Theoretical study of the novel sandwich compound [Au<Subscript>3</Subscript>Cl<Subscript>3</Subscript>Tr<Subscript>2</Subscript>]<Superscript>2+</Superscript>

A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au₃Cl₃Tr₂]²⁺ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet. Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level     

<Emphasis Type="Italic">Ab initio</Emphasis> and DFT investigation of electrophilic addition reaction of bromine to <Emphasis Type="Italic">endo,endo</Emphasis>-tetracyclo[4.2.1.1<Superscript>3,6</Superscript>.0<Superscript>2,7</Superscript>]dodeca-4,9-diene

Full geometric optimization of endo,endo-tetracyclo[4.2.1.1^3,6.0^2,7]dodeca-4,9-diene (TTDD) has been carried out by ab initio and DFT/B3LYP methods and the structure of the molecule investigated. The double bonds of TTDD molecule are endo pyramidalized. The structure of π-orbitals and their mutual interactions for TTDD molecule were investigated. The cationic intermediates and products obtained as a result of the addition reaction have been studied using the HF/6-311G(d), HF/6-311G(d,p) and B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable N- and U-type cations and the difference between the stability of these cations is small. The N- and U-type reaction products are obtained as a result of the reaction, which takes place via the cations in question. The stability of exo, exo and exo, endo isomers of N-type product are nearly the same and the formation of both isomers is feasible. The U-type product basically formed from the exo, exo-isomer. Although the U-type cation was 0.68 kcal mol⁻¹ more stable than the N-type cation, the U-type product was 4.79 kcal mol⁻¹ less stable than the N-type product. Figure The energy diagram of TTDD–Br₂ system (kcal mol⁻¹)(MP2/6-311G*//HF/6-311G*)     

<Superscript>18</Superscript> O-rich Oxygen from Land Photosynthesis

ATMOSPHERIC oxygen is not in equilibrium with sea water with respect to the isotope exchange illustration but has an ¹⁸O excess of about 22‰ compared to sea water¹. This could be due to isotope fractionation during respiration². Another large contribution to the effect has been overlooked up to now. Photosynthesis on land takes place in transpiring leaves, where the difference in the vapour pressure of ¹⁶OH₂ and ¹⁸OH₂ concentrates the heavy molecules in their stationary water content. Since the free oxygen stems from the water in which photosynthesis takes place^3–8 (with only a very small shift in isotopic composition⁹), photosynthesis on land is an ¹⁸O source for atmospheric O₂. We have begun to study this effect quantitatively.

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Theoretical study of the intermolecular H-bonding and intermolecular proton transfer between isocytosine tautomeric forms and <Emphasis Type="Italic">R</Emphasis>,<Emphasis Type="Italic">S</Emphasis>-lactic acid

Eight H-bonded complexes between isocytosine (isoC) tautomeric forms and R/S-lactic acid (LA) have been studied at the B3LYP and HF levels of theory using 6–31+G(d) basis set. The energy barriers of the intermolecular proton transfers were also estimated as the results showed that they are several times lower than those of the intramolecular proton transfers of isoC in the gas phase. Furthermore, the energy barriers of the tautomerizations in which the carboxylic H-atom takes part are several times lower than those in which the LA OH group assists the proton transfer. Figure     

Methylenecyclopropene: local vision of the first <Superscript>1</Superscript>B<Subscript>2</Subscript> excited state

The ¹A₁ ground and the first ¹B₂ excited states of the methylenecyclopropene (triafulvene) are described by localized wave functions, based on 20 structures valence bond structures. The results are compared to CASSCF(4,4) calculations for both the energetics and the dipole moment. Additional calculations with partial electronic delocalization are presented, and it is shown that the dipole moment modification does not correspond to a situation where the antiaromatic situation prevails (with 4n electrons in the cycle). Part of the analysis uses a “trust factor” that helps to decide if a wave function is appropriate to describe a given state. The trust factor compares the VB wave function to the CASSCF’s with their overlap. Finally, the valence bond density is used to produce density maps that illustrate the electron transfer upon excitation.

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Graphical Abstract A projector-based method compares CASSCF wave functions to local wave functions, including Lewis structures as shown in the picture. A “trust factor” (τ) is obtained. Both the ground state and the first excited state of the methylenecyclopropene are discussed

     

Cell wall polysaccharides isolated from the fungus <Emphasis Type="Italic">Neotestudina rosatii</Emphasis>, one of the etiologic agents of mycetoma in man

The alkali-extractable water-soluble polysaccharides F1SS isolated from the cell wall of two isolates of the pathogen Neotestudina rosatii and one of Pseudophaeotrichum sudanense, which is now considered as a synonym of the former, have been studied by methylation analysis, GC–MS and NMR spectroscopy. The three polysaccharides differ mainly in their content in galactofuranose, and have the following idealized repeating unit:      

Critical test of some computational methods for prediction of NMR <Superscript>1</Superscript>H and <Superscript>13</Superscript>C chemical shifts

Performance of 18 DFT functionals (B1B95, B3LYP, B3PW91, B97D, BHandHLYP, BMK, CAM-B3LYP, HSEh1PBE, M06-L, mPW1PW91, O3LYP, OLYP, OPBE, PBE1PBE, tHCTHhyb, TPSSh, wB97xD, VSXC) in combinations with six basis sets (cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, IGLO-II, and IGLO-III) and three methods for calculating magnetic shieldings (GIAO, CSGT, IGAIM) was tested for predicting ¹H and ¹³C chemical shifts for 25 organic compounds, for altogether 86 H and 88 C atoms. Proton shifts varied between 1.03 ppm to 12.00 ppm and carbon shifts between 7.87 ppm to 209.28 ppm. It was found that the best method for calculating ¹³C shifts is PBE1PBE/aug-cc-pVDZ with CSGT or IGAIM approaches (mae?=?1.66 ppm), for ¹H the best results were obtained with HSEh1PBE, mPW1PW91, PBE1PBE, CAM-B3LYP, and B3PW91 functionals with cc-pVTZ basis set and with CSGT or IGAIM approaches (mae?=?0.28 ppm). We found that often larger basis sets do not give better results for chemical shifts. The best basis sets for calculating ¹H and ¹³C chemical shifts were cc-pVTZ and aug-cc-pVDZ, respectively. CSGT and IGAIM NMR approaches can perform really well and are in most cases better than popular GIAO approach.

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Graphical Abstract Mean absolute errors for ¹H and ¹³C chemical shifts and computational times of neutral toluene molecule with aug-cc-pVDZ basis set and CSGT approach

     

First report of a planar and a quasi-planar Al<Subscript>13</Subscript><Superscript>+</Superscript> cluster having localized antiaromatic deltas within an aromatic sea: NICS,ELF, AIM,and AdNDP bonding analysis

A perfectly planar Al₁₃⁺ cluster (CI) and a quasi-planar Al₁₃⁺ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.

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Graphical abstract Planar and quasi-planar Al₁₃⁺ clusters with triangular core surrounded by a ring of ten atoms.

     

Structural characterization of the exopolysaccharide PS-EDIV from <Emphasis Type="Italic">Sphingomonas pituitosa</Emphasis> strain DSM 13101

Members of the bacterial genus Sphingomonas are known to produce highly viscous polysaccharides in solution. The exopolysaccharide PS-EDIV was produced by Sphingomonas pituitosa strain DSM 13101, purified using centrifugation, and precipitation and its structure was elucidated by 1D and 2D NMR techniques and chemical microderivatization combined with various mass spectrometric techniques. The following repeating unit of the polysaccharide could be identified: In addition, the polysaccharide also contains acetyl and glyceryl groups whose exact positions were not determined. PS-EDIV is similar in structure to a known exopolysaccharide but differs in being the first bacterial polysaccharide in which two different glucuronic acids are combined. It caused a high viscosity of the culture broth after cultivation for 48 h, although a gelation was not observed.     

Conformational exchange of aromatic side chains by <Superscript>1</Superscript>H CPMG relaxation dispersion

Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic ¹³C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic ¹H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly ¹H and ¹³C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1. The method has been validated by measuring fast folding–unfolding kinetics of the small protein CspB under native conditions. The determined rate constants and populations agree well with previous results from ¹³C CPMG relaxation dispersion experiments. The CPMG-derived chemical shift differences between the folded and unfolded states are in good agreement with those obtained directly from the spectra. In contrast, the ¹H relaxation dispersion profiles in phenylalanine, tyrosine and the six-ring moiety of tryptophan, display anomalous behavior caused by ³J ¹H–¹H couplings and, if present, strong ¹³C–¹³C couplings. Therefore they require site-selective ¹H/²H and, in case of strong couplings, ¹³C/¹²C labeling. In summary, aromatic ¹H CPMG relaxation dispersion experiments work on certain positions (His δ2, His ε1 and Trp δ1) in uniformly labeled samples, while other positions require site-selective isotope labeling.

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Molecular docking study of the binding of aminopyridines within the K<Superscript>+</Superscript> channel

We present a molecular docking study aimed to identify the binding site of protonated aminopyridines for the blocking of voltage dependent K⁺ channels. Several active aminopyridines are considered: 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, 3,4-diaminopyridine, and 4-aminoquinoleine. We apply the AutoDock force field with a lamarckian genetic algorithm, using atomic charges for the ligands derived from the electrostatic potential obtained at the B3LYP/cc-pVDZ level. We find a zone in the α-subunit of the K⁺ channel bearing common binding sites. This zone corresponds to five amino acids comprised between residuals Thr107 and Ala111, in the KcsA K⁺ channel (1J95 pdb structure). The 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine bind to the carboxylic oxygens of Thr107 and Ala111. In all cases aminopyridines are perpendicular to the axis of the pore. 4-aminoquinoleine binds to the carboxylic oxygen of Ala111. Due to its large size, the molecular plane is parallel to the axis of the pore. The charge distributions and the structures of the binding complexes suggest that the interaction is driven by formation of several hydrogen bonds. We find 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine with similar binding energy. Considering the standard error of the estimate of the AutoDock force field, this energy should lie, as a rough estimation, in the interval 3–7 kcal mol⁻¹. On the other hand, 4-aminoquinoleine seems to have a smaller binding energy. Figure Three-dimensional structure of the complex between 4-AQH⁺ and the binding sites of the K⁺ pore. Only the amino acid sequence from Thr107 to Ala111 is considered. Two different representations are included. In the left, the Thr107 position is marked. The right representation shows the CO oxygens of the peptide bond as spacefilled structures.     

BODIPY for photodynamic therapy applications: computational study of the effect of bromine substitution on <Superscript>1</Superscript>O<Subscript>2</Subscript> photosensitization

Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet–triplet energy gaps, and spin–orbit matrix elements were computed and are discussed here. The effects of bromine substitution on the photophysical properties of BODIPY were elucidated. The investigated compounds were found to possess different excited triplet states that lie below the energy of the bright excited singlet state (S₁ or S₂), depending on the positions occupied by the bromine atoms. The computed spin–orbit matrix elements for the radiationless intersystem crossing S_n?→ ?T_m and the relative singlet–triplet energy gaps allowed the prediction of plausible nonradiative decay pathways for the production of singlet excited molecular oxygen, the key cytotoxic agent in photodynamic therapy.

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Graphical Abstract The photophysical properties affected by the presence of bromine atoms in different positions of a BODIPY core have been here elucidated. In particular it has been found that SOC values strongly depend on the position of heavy atoms into the BODIPY core, suggesting positions 1 and 7 as the best ones to enhance the ISC kinetics

     

The platinum-olefin binding energy in series of (PH<Subscript>3</Subscript>)<Subscript>2</Subscript>Pt(olefin) complexes - a theoretical study

Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics bearing coordinated olefins with general formula (R¹R²C = CR³R⁴)Pt(PH₃)₂ [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin substituents. Figure Representation of (CH₂ = CHR)Pt(PPh₃)₂ and the stability chart     

ATP and its N<Superscript>6</Superscript>-substituted analogues: parameterization,molecular dynamics simulation and conformational analysis

In this work we used a combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of 12 adenosine triphosphate (ATP) analogues in a water environment. We present simulations in AMBER force field for ATP and 12 published analogues [Shah et al. (1997) Proc Natl Acad Sci USA 94: 3565–3570]. The calculations were carried out using the generalized Born (GB) solvation model in the presence of the cation Mg²⁺. The ion was placed at a close distance (2 Å) from the charged oxygen atoms of the beta and gamma phosphate groups of the ?3 negatively charged ATP analogue molecules. Analysis of the results revealed the distribution of inter-proton distances H8–H1′ and H8–H2′ versus the torsion angle ψ (C4–N9-C1′–O4′) for all conformations of ATP analogues. There are two gaps in the distribution of torsion angle ψ values: the first is between ?30 and 30 degrees and is described by cis-conformation; and the second is between 90 and 175 degrees, which mostly covers a region of anti conformation. Our results compare favorably with results obtained in experimental assays [Jiang and Mao (2002) Polyhedron 21:435–438].

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Figure Dihedral O4′–C1′–N9–C4 angle dependence on inter-proton distances H8–H1′ (crosses) and H8–H2′ (dots) measured for ATP

     

Isolation and structural determination of a unique polysaccharide containing mannofuranose from the cell wall of the fungus <Emphasis Type="Italic">Acrospermum compressum</Emphasis>

The alkali-extractable and water-soluble fungal polysaccharide F1SS isolated from the cell wall of Acrospermum compressum has been studied by methylation analyses, reductive cleavage and 1D- and 2D-NMR spectroscopy. The polysaccharide consists of a regular disaccharide repeating unit with the structure: The mannan core was obtained by mild hydrolysis of the polysaccharide F1SS and its structure was deduced to be composed of a skeleton of α-(1→6)-mannopyranan, with around 1 out of 11 residues substituted at position 2 by short chains (one to six units) of 2-substituted mannopyranoses. DOSY experiments provided molecular sizes of 60 kDa and 2.5 kDa for the polysaccharide F1SS and the mannan core, respectively. This is the first report of a fungal mannofuranose-containing cell wall polysaccharide.     

Molecular modeling and biophysical analysis of the c-MYC NHE-III<Subscript>1</Subscript> silencer element

G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III₁ (nuclease hypersensitivity element III₁) from two 39-base complementary sequences. The NHE modeled here consists of single folded conformers of the polypurine intramolecular G-Quadruplex and the polypyrimidine intramolecular i-Motif structures, flanked by short duplex DNA sequences. The G-Quadruplex was based on published NMR structural data for the c-MYC 1:2:1 loop isomer. The i-Motif structure is theoretical (with five cytosine–cytosine pairs), where the central intercalated cytosine core interactions are based on NMR structural data obtained for a tetramolecular [d(A₂C₄)₄] model i-Motif. The loop structures are in silico predictions of the c-MYC i-motif loops. The porphyrin meso-tetra(N-methyl-4-pyridyl)porphine (TMPyP4), as well as the ortho and meta analogs TMPyP2 and TMPyP3, were docked to six different locations in the complete c-MYC NHE. Comparisons are made for drug binding to the NHE and the isolated G-Quadruplex and i-Motif structures. NHE models both with and without bound cationic porphyrin were simulated for 100 ps using molecular dynamics techniques, and the non-bonded interaction energies between the DNA and porphyrins calculated for all of the docking interactions. Figure Molecular models of the average structure of the final 20 ps of the molecular dynamics simulation of the c-MYC NHE-III₁ (nuclease hypersensitivity element III₁) “silencer” element. The G-Quadruplex structure is at the top-center, and the i-Motif is at the bottom-center of each picture. a “Rotation #1” of the G-Quadruplex, with the T15 loop at the top and rear and the G19/A20 loop at the top and front of the picture. b “Rotation #2” of the G-Quadruplex, with the T15 loop at the top and front of the image, and the G19/A20 loop at the front and adjacent to the G-Quadruplex/i-Motif interface     

Molecular models of protein kinase 6 from Plasmodium falciparum

Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria. Figure Ribbon diagram of PfPK6 complexed with a roscovitine and b olomoucine     

Mechanistic study of palladium-catalyzed telomerization of 1,3-butadiene with methanol

The Pd-catalyzed telomerization in the presence of phosphine and carbene ligands has been computed. It is shown that the C–C coupling of the less stable complex A with one trans- and one cis-butadiene in syn orientation forms the most stable intermediate B and is favorable both kinetically and thermodynamically. Protonation of B leads to equilibrium of the two most stable isomers of intermediate C. The overall regioselectivity is favored thermodynamically.      

Potential Management of <Emphasis Type="Italic">Chamaedorea seifrizii</Emphasis> (Palmae), a Non-timber Forest Product from the Tropical Forest of Calakmul,Southeast Mexico<Superscript>1</Superscript>

Potential Management of Chamaedorea seifrizii (Palmae), a Non-timber Forest Product from the Tropical Forest of Calakmul, Southeast Mexico. Leaves and seeds of Chamaedorea (xate) palms are important non-timber forest products (NTFPs). In the Calakmul region (Yucatan Peninsula) of Mexico, several communities have sporadically collected and sold seeds of C. seifrizii since 1980. However, harvesting has intensified recently, raising concerns about overexploitation. To evaluate the economic potential of leaf and seed exploitation in the area, we collected information on abundance, population patterns, and leaf and seed stocks in Ejido Conhuas, a community within the Calakmul Biosphere Reserve (CBR). Then we combined these data with current market values and hypothetical management regimes obtained from the literature for leaves and seeds. Conducting a quantitative analysis of 43 0.1^ha plots with differences in forest and soil type, we assessed the abundance of C. seifrizzi in the area. We also conducted interviews to estimate the importance of xate in the local economy. We found C. seifrizii density to be highly variable, with a mean (±SE) of 295 (±35), with forest type being the most influential factor. Population structures differ between forest types, with healthy populations in medium and lower forest. We found a mean density of leaves of harvestable size of 3,750 (±380) leaves ha^-1, while seed production was 1.5 (±0.3) kg/ha^-1 of fresh seeds. Assuming sustainable harvest rates of 30–50% for leaves and 80% for seeds, one hectare of forest could generate USD 7.0–15.9/ha^-1. Considering the number of households (102) and 10% of the total area managed each year (5,700 ha), this harvest could generate a household income of USD 391–838 annually. At the moment, xate trade represents a minor component in the economy of the community, but given the area’s extensive forest (>57,000 ha), the resource abundance, and the low human population, we believe the NTFPs derived from C. seifrizii have a potentially great economic impact in the area.