Mol Energy Research Articles

Larvicidal and antiviral nature of phoenix dactylifera L. natural products by targeting dengue virus and Aedes aegypti L. Proteins through molecular docking

Mosquito-borne infections are a global health threat. Different species of mosquitoes transmit viruses and cause several human diseases. In this study, in silico molecular docking of 23 phytochemicals of Phoenix dactyliferawas performed to look for potential hits that bind effectively at the active site of different protein targets of the dengue virus (2FOM, 3U1I, and 2BMF) and Aedes aegypti mosquito (1YIY, 1PZ4 and 3UQI). The docking results of coumestrol to 2FOM resulted in four hydrogen bonds and ten hydrophobic interactions with binding energy of −9.5 kcal/mol. Similarly, the docking simulation of 2FOM to pinoresinol formed seven covalent bonds resulting in − 9.5 kcal/ mol energy. There were also two hydrophobic (THR289 and THR450) and one π-cation (LYS515) interactions with amino acid residues. Similarly, isofucosterol exhibited the best binding conformations with the lowest binding energy values with the two target proteins 1YIY and 1PZ4 of Ae.egyptia. The docking simulation of 1YIY to isofucosterol resulted in one hydrogen bond with binding energies of – 10.3 kcal/mol and 16 hydrophobic interactions with different amino acid residues. A similar observation of target protein 1PZ4 was noted in isofucosterol resulting in −9.7 kcal/mol energy. From the docking studies reported in this paper, promising candidates can be further optimized and studied in vitro.

Nonsphericity in diferratetracarbaboranes having 2n + 2 Wadean skeletal electrons: deviations from closo deltahedral geometries and high-energy kinetically stable isomers.

The diferratetracarbaboranes Cp2Fe2C4Bn-6Hn-2 (n = 10 to 14; Cp = η5-C5H5) as well as the experimentally known C-tetramethyl derivatives Cp2Fe2C4Me4B8H8 have been studied by density functional theory methods. For the Cp2Fe2C4Me4B8H8 system, the three structurally characterized isomers produced under relatively mild conditions having an "open" tetragonal or pentagonal face correspond to the lowest energy structures not based on the 14-vertex closo deltahedron, namely the bicapped hexagonal antiprism. These structures provide examples of kinetically favored but thermodynamically disfavored high-energy metallacarborane structures. Thus the lowest energy such structure lies ∼22 kcal mol-1 above the global minimum, namely a C2vcloso structure with no C-C deltahedral edges. This latter global minimum 14-vertex closo structure is found experimentally to be the ultimate pyrolysis product in the Cp2Fe2C4Me4B8H8 system at 300 °C. The lowest energy structures for the smaller 11 to 13 vertex Cp2Fe2C4Bn-6Hn-2 systems are the corresponding most spherical closo deltahedra as expected by the Wade-Mingos rules for these 2n + 2 skeletal electron systems. However, for the 11- and 12-vertex systems, less spherical deltahedral structures providing additional degree 6 vertices for the iron atoms and degree 4 vertices for the carbon atoms become energetically competitive. For the 10-vertex Cp2Fe2C4B4H8 system a relatively non-spherical deltahedral structure with four degree 4 vertices for the carbon atoms and two degree 6 vertices for the iron atoms is energetically preferred by a substantial margin. Thus such a structure lies ∼23 kcal mol-1 in energy below the isomeric 10-vertex closo bicapped tetragonal antiprism structure expected from the Wade-Mingos rules for this 2n + 2 skeletal electron system.

Tetracarbaboranes: nido structures without bridging hydrogens.

The structures and energetics of the tetracarbaboranes C4Bn-4Hn (n = 6 to 13) have been investigated by density functional theory and coupled cluster calculations. In general, the lowest energy structures of the tetracarbaboranes C4Bn-4Hn minimize the number of C-C polyhedral edges as well as the degrees of the carbon vertices. For the C4B2H6 and C4B3H7 systems the lowest energy structures are pyramidal structures having all four carbon atoms located on the base of the pyramid. The lowest energy structure for the 9-vertex C4B5H9 system is a capped square antiprism. The frameworks of the lowest energy C4B4H8 and C4B6H10 structures resemble those of the isoelectronic experimentally known B8H12 and B10H14 structures. However, an experimentally known S4 adamantane-like 10-vertex structure found in Me4C4B6Et6 based on a tetracapped octahedron lies only ∼7 kcal mol-1 in energy above the lowest energy structure. The lowest energy structures for the 11- to 13-vertex C4Bn-4Hn (n = 11, 12, 13) systems can be derived from an (n + 1)-vertex closo deltahedron by removing a high-degree vertex. At least three of the four carbon atoms are located on edges of the resulting pentagonal or hexagonal open face in the low-energy structures. However, the structures of the experimentally known R4C4B8H8 (R = Me, Et) obtained from the dimerization of R2C2B4H42- differ from these low-energy structures. The Me4C4B8H8 polyhedron has a C4 chain and two tetragonal faces whereas the Et4C4B8H8 polyhedron has a hexagonal face with two C2 units. These structures lie within 2 kcal mol-1 of each other thereby accounting for the fluxional properties of these systems observed by NMR spectroscopy.

Proton Exchanges between Phenols and Ammonia or Amines: A Computational Study

Density functional theory calculations at the B3LYP/6-31+G(d,p) level of theory have been performed to explore proton exchanges between phenols and ammonia or amines, which can be used to account for previous NMR experiments. For the parent phenol-NH(3) system, a transition state with a symmetric phenolate-NH(4)(+)-like structure, which lies about 35 kcal mol(-1) in energy above the hydrogen-bonded complex, has been successfully located. An intrinsic reaction coordinate (IRC) analysis indicates that the proton exchange is a concerted process, which can be roughly divided into four continuous subprocesses. A series of para-substituted phenol-NH(3) systems have been considered to investigate the substituent effect. Whereas introduction of an electron-withdrawing group on the phenol appreciably reduces the barrier, an opposite effect is observed for an electron-donating group. Moreover, it has been disclosed that there exists a good linear correlation between the activation barriers and the interaction energies between the phenols and NH(3), indicating the important role of proton transfer (or hydrogen bonding) in determining the proton exchange. Also considered are the proton exchanges between phenol and amines and those for some sterically hindered systems. The results show that the phenol tends to exchange hydrogen with the amines, preferably the secondary amines, and that the steric effect is favorable for the proton exchange, which imply that, as the IRC analysis suggested, besides the proton transfer, the flip of the ammonium-like moiety may play a significant role in the course of proton exchange. For all of these systems, we investigated the solvent effects and found that the barrier heights of proton exchange decrease remarkably as compared to those in a vacuum due to the ion pair feature of the transition state. Finally, we explored the phenol radical cation-NH(3) system; the barrierless proton transfer and remarkably low barrier (5.2 kcal mol(-1)) of proton exchange provide further evidence for the importance of proton transfer in the proton exchange.

Force-induced melting of a short DNA double helix.

The dynamic behaviour of DNA is of fundamental importance to many cellular processes. One principal characteristic, central to transcription and replication, is the ability of the duplex to "melt". It has recently been shown that dynamic force spectroscopy provides information about the energetics of biomolecular dissociation. We have employed this technique to investigate the unbinding of single dodecanucleotide molecules. To separate the duplex to single-stranded DNA, forces ranging from 17 to 40 pN were required over a range of loading rates. Interpretation of the dependence of melting force on loading rate revealed that the energy barrier to rupture is between 9 and 13 kcal mol-1 in height and situated 0.58 nm from an intermediate structural state. Thermal melting studies show that, prior to dissociation, the oligonucleotide underwent a transition which required between 7 and 11 kcal mol-1 in energy. Through combined dynamic force spectroscopy and thermal melting studies we show the derivation of an energy landscape to dissociate a 12-mer duplex. Until very recently, this type of information was only accessible by computational analysis. Additionally, the force spectroscopy data allow an estimation of the kinetics of duplex formation and melting.

Reorientational Dynamics of Cyclohexadienyl Radicals in High-Silica ZSM-5

The avoided-level-crossing relaxation of a polarized muon spin-label was used to investigate the reorientational dynamics of muonated cyclohexadienyl radicals in NaZSM-5 with SiO2/Al2O3 ratios of 670 and 900 and loadings of one and two benzene molecules per unit cell. It was found that on a critical time scale of about 50 ns the radical performs fast uniaxial rotation about the axis perpendicular to the molecular plane. Superimposed on this there is a two-site jump motion between two orientations that differ by an angle of 110° and 1.0 kJ mol-1 in energy. This causes increasing averaging of the orientations above 50 K. It is particularly extensive but still not isotropic in a temperature range between 200 and 450 K. Below 50 K, the uniaxial rotation slows down below the critical time scale of the experiment, and below 20 K any motion is frozen. It is suggested that such a high reorientational mobility is possible only for the radicals occupying sites at the channel intersections. Above ca. 450 K, the reve...

Collisional Attenuation of Focused CH3Cl Molecular Beams in a Hexapole Filter

The attenuation of hexapole-focused CH3Cl molecular beams has been studied as a function of inert gas and nitrogen gas pressure in a hexapole-collision cell. Cross sections have been determined as a function of relative velocity, using seeded beams, and as a function of specific |JKM〉 states through variation of the electric field strength in the hexapole. Beam attenuation is attributed to rotationally inelastic collisions in which a beam molecule following a focusing upper Stark state (KM 0), which then follows a modified, nonfocusing trajectory and is lost from the beam. Experimental cross sections are in the range from 200 to 670 A2, consistent with collisions controlled by a long-range interaction (8 to 15 A) involving the transfer of a few J mol-1 of energy. Collision cross sections estimated using a van der Waals interaction potential with dispersion and dipole−ind...

Structure, Spectra, and Reaction Energies of the Aluminum−Phosphorus Rings (HAl−PH)2 and (H2Al−PH2)2 and the (HAl−PH)4 Cluster

Recently a six-membered ring consisting of three coordinate aluminum and phosphorus was synthesized, as well as an R2AlPR‘2 compound of three coordinate aluminum and phosphorus. This research was initiated in order to better understanding the bonding in these new compounds, as well as the more common compounds that contain four coordinate aluminum and phosphorus. Ab initio investigations of the structure, bonding, vibrational spectra, and reaction energies for the unknown three coordinate ring (HAl−PH)2, the four coordinate ring (H2Al−PH2)2, and the four coordinate cluster (HAl−PH)4 are presented. The three coordinate ring has two conformers that are within 3 kcal mol-1 in energy. The higher energy conformer is planar and the P−H bonds are trans, while the other is puckered and the P−H bonds are cis. The theoretical Al−P bond lengths are within 0.01 Å of the experimental values for the three coordinate Al−P compounds, despite the size difference between the hydrogen atoms of the model compound and the substituents on the experimentally determined structures. The structures for (H2Al−PH2)2 and for the (HAl−PH)4 cube are also in good agreement with analogous known compounds. The theoretical energies of H2 loss and dimerization to form the cube compound from an initial Lewis acid−base adduct are also reported. The laboratory synthesis of (RAl−PR‘)2 compounds should be possible.

Endothermicity or exothermicity of water/alcohol mixtures

Excess enthalpies of mixtures of water with methanol, ethanol, 1- and 2-propanol, 1-, 2- and tert-butanol were determined by dilution calorimetry in the accessible range of mole fractions at 25-degrees-C. Ab initio RHF calculations were performed on the alcohols, their dimers and complexes with water. A full optimisation at the 6-31G level was used to obtain the properties of interest of these systems. The calculated H-bond energies are similar for all the studied alcohols. Nevertheless, a systematic stabilisation of the mixed dimers is found, especially for the secondary and tertiary alcohols. The formation of mixed H-bond chains is exothermic and does not follow the rules of the geometric mean. To a first approximation, the experimental excess enthalpies DELTAH(e) for all the systems follow the equation DELTAH(e) = C6/1X(W)6X(A) + C1/1X(W)X(A) + C1/2X(W)X(A)2 The calorimetric results may be explained by the presence in water of two kinds of H-bonds differing by about 8.3 kJ mol-1 in energy. Upon dilution in water, the alcohol is inserted in a weak chain and renders the adjacent water-bond strong. As a consequence, the dilution of an alcohol in water is always exothermic. The dilution of water in an alcohol causes stabilisation of the H-bonds but has a negative effect on the non-specific cohesion. The effect of the non-specific forces increases in the homologous series, making the dissolution of water in the alcohols endothermic starting from propanol. The stabilisation of H-bonds formed by water at high dilution in the alcohols increases according to the sequence: primary < secondary < tertiary.

Heat Capacity and Thermodynamic Properties of Poly(Vinyl Chloride).

Heat capacities, C p , of three different samples of poly(vinyl chloride), PVC, have been determined from 6 to 375 K by adiabatic calorimetry. These three samples were derived from either bulk- or suspension-polymerization processes and were measured either as received or after pelleting under pressure. The heat capacities of the samples are almost identical if the thermal and pressure histories are the same. Below the glass transition temperature, T g , of about 355 K, C p of PVC was found to be exceptionally linear over a wide temperature range. C p of annealed PVC may be represented by (10 + 0.166 T) J K-1 mol-1 to within 1 percent of the measured values from 80 to 340 K. Approximately 200 J mol-1 of energy were stored in the samples by the pelleting processes. The stored energies begin to release at about 30 to 40 K below the glass transition temperature. T g for powdery or relaxed samples occurs around 352 to 356 K for the suspension-polymerized PVC sample and 348 to 351 K for bulk-polymerized sample.