Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals

Experimental and theoretical studies of electron densities and the corresponding derived entities such as electrostatic potentials have been the primary means of understanding the chemical nature and electronic properties of crystalline substances. Conventional crystal calculation methods such as the embedded cluster models are capable of performing calculations on small and medium-sized molecules, while periodic ab initio methods can treat crystals with up to 200 atoms per unit cell. A linear scaling method, viz. the molecular tailoring approach, has recently been developed for obtaining ab initio quality one-electron properties. In the present study, the molecular tailoring approach is employed to generate electron density, electrostatic potential and interaction density maps with the ibuprofen crystal as a test case. The interaction density and electrostatic potential maps produced in the present work succinctly bring out the actual crystalline environment around a given reference molecule by including the interactions with atoms in its neighborhood. The results obtained from the molecular tailoring approach may thus be expected to enhance our understanding of the environment in the crystalline material with reasonably small computational effort.Contribution to the Jacopo Tomasi Honorary Issue     

Molecular hydrogen "pairing" interaction in a metal organic framework system with unsaturated metal centers (MOF-74)

Infrared (IR) absorption spectroscopy measurements of molecular hydrogen in MOF-74-M (M = metal center) are performed as a function of temperature and pressure [to 45 kTorr (60 bar) at 300 K, and at lower pressures in the 20-200 K range] to investigate the nature of H(2) interactions with the unsaturated metal centers. A small shift (～?-30 cm(-1) with respect to the unperturbed H(2) molecule) is observed for the internal stretch frequency of H(2) molecules adsorbed on the metal site at low loading. This finding is in contrast to much larger shifts (～?-70 cm(-1)) observed in previous studies of MOFs with unsaturated metal centers (including MOF-74) and the general assumption that H(2) stretch shifts depend on adsorption energies (FitzGerald et al., Phys. Rev. B 2010, 81, 104305). We show that larger shifts (～?-70 cm(-1)) do occur, but only when the next available site ("oxygen" site) is occupied. This larger shift originates from H(2)-H(2) interactions on neighboring sites of the same pore, consistent with the short distance between H(2) in these two sites ～2.6 ? derived from an analysis of neutron diffraction experiments of D(2)-D(2) at 4 K (Liu et al., Langmuir 2008, 24, 4772-4777). Our results at 77 K and low loading can be explained by a diffusion barrier against pair disruption, which should be enhanced by this interaction. Calculations indicate that the vibrational shifts do not correlate with binding energies and are instead very sensitive to the environment (interaction potential and H(2)-H(2) interactions), which complicates the use of variable temperature IR methods to calculate adsorption energies of specific adsorption sites.     

Spectroscopic investigation of the charge-transfer interactions between 1,4,7-trimethyl-1,4,7-triazacyclononane and the acceptors iodine, TCNE, TCNQ and chloranil

The interaction of the interesting polynitrogen cyclic base 1,4,7-trimethyl-1,4,7-triazacyclononane (TMTACN) with the sigma-acceptor iodine and pi-acceptors tetracyanoethylene (TCNE), 7,7,8,8-tetracyanoquinodimethane (TCNQ) and tetrachloro-p-benzoquinone (chloranil) have been studied spectrophotometrically and cyclic voltametrically in chloroform at 20 degrees C. Based on the obtained data, the formed charge-transfer complexes were formulated as [(TMTACN)I](+).I(3)(-), [(TMTACN)(TCNE)(5)], [(TMTACN)(TCNQ)(3)] and [(TMTACN)(chloranil)(3)] where the stoichiometry of the reactions, donor:acceptor molar ratios, were shown to equal 1:2 for iodine complex, 1:3 for chloranil and TCNQ complexes and 1:5 for TCNE complex.     

Theoretical study of selenium and tellurium impurities in (ZnO)6 clusters using DFT and TDDFT

Zinc oxide (ZnO) nanostructures have attracted much interest due to their potential applications in various fields including optoelectronics, glass industries, and solar cells. These compounds hold the promise of creating new materials that can advance energy technologies. In this work, a series of (ZnO)₆ clusters with selenium and tellurium applied as substitutional impurities has been studied. The investigated structures have been produced through the doping of (ZnO)₆ clusters by replacing an oxygen atom with a selenium or a tellurium atom at each time. The ground state geometric parameters of (ZnO)₆ structures, containing selenium or tellurium atoms as substitutional impurities, were calculated using density functional theory (DFT) with B3LYP and LanL2DZ basis set. Excited state energies and absorption wavelengths were computed using time‐dependent‐DFT (TDDFT). For the calculation of emission wavelengths, Hartree–Fock configuration interaction singles (HF/CIS) has been used in order to perform the excited state geometry optimization. This work led to some important results that can be helpful for developing novel THz sensitive materials and imaging detectors that may be an alternative to x‐rays detectors for radiology as well as for the development of solar cells and electroluminescent diodes. Zinc oxide (ZnO) nanostructures have attracted growing interest due to their potential applications in many technological fields, including optoelectronics, the glass industry, and energy. The presence of impurities, in particular selenium and tellurium, in ZnO‐based clusters can affect their structural and spectroscopic properties. Some of these doped nanostructures have favorable Terahertz emission characteristics that make them good candidates for applications in biology and medicine.     

Sustainable and efficient flame retardant materials for achieving high fire safety for polystyrene composites

Journal of Thermal Analysis and Calorimetry - Novel porous carbon sheets were developed as green, renewable, cost-effective, and efficient flame retardant material for thermoplastic polymers....     

Gamma-ray and sunlight-induced synthesis of silver nanoparticles using bacterial cellulose and cell-free filtrate produced by Komagataeibacter rhaeticus N1 MW322708 strain

Cellulose - Antibacterial coatings based on bacterial cellulose (BC) have been widely used in many fields including food packaging and wound dressing. In this study, we aimed to synthesis of...     

Computational Design,Synthesis and Application of a New Selective Molecularly Imprinted Polymer for Electrochemical Detection

A computational approach was developed to find a suitable functional monomer to design a new molecularly imprinted polymer (MIP), based on which methacyrlic acid (MAA) was selected as a functional monomer to synthesize the molecular imprinted and non‐imprinted polymers. All calculations were carried out using Gaussian 03 software based on the application of Hartree?Fock (HF) method with 6‐31G (d) basis set. The performance of the MIPs prepared with different ratios of MAA was then evaluated using equilibrium rebinding assays. The MIP with the highest binding capacity was chosen as recognition material for the fabrication of new PVC sensors and their responses were compared with each other and with previously reported modifiers in literature. The addition of the ionic surfactant (TFPB) was found to have a synergistic effect on the response mechanism of the electrodes. The results of the MIP modified sensors show that they provide an improved electrode slope, wider pH range and a highly extended life time reaching 7 months compared to 2–4 weeks in case of traditional ion‐exchangers reported in literature, besides, being successfully applied for measurements in biological samples.     

Purification of DNA-derived deoxynucleotides from leukocytes involving nuclease elution of an ion-exchange column

A method has been developed in which the DNA of leukocytes (as the buffy coat from blood) is isolated in the form of its constituent deoxynucleotides. The steps in this method are as follows: (1) lyse the leukocytes with sodium dodecyl sulfate (SDS) and enzymatically digest the proteins and RNA, (2) remove the SDS on a non-polar adsorbent (Bio-Beads SM-4) and then trap the DNA on a quaternary amine silica cartridge, (3) wash the column with 1 M NaCl-buffer, (4) digest the DNA on the column with staphylococcal nuclease and (5) elute the digested DNA with 0.5 M NaCl-buffer and digest it further with bovine spleen phosphodiesterase II to deoxynucleotide-3′-monophosphates. From a 40-μl sample of butty coat was obtained 126 ± 14 μg (two experiments, eight sample total) of deoxynucleotides. Reversed-phase high-performance liquid chromatography, which removed the added enzymes, showed only peaks for deoxynucleotides. For comparison, the amount of deoxynucleotides obtained from the leukocytes by an automated phenol extraction procedure was 101 ± 5.4 μg (one experiment in triplicate).     

A discontinuous Galerkin method for time fractional diffusion equations with variable coefficients

We propose a piecewise-linear, time-stepping discontinuous Galerkin method to solve numerically a time fractional diffusion equation involving Caputo derivative of order μ ∈ (0, 1) with variable coefficients. For the spatial discretization, we apply the standard continuous Galerkin method of total degree ≤ 1 on each spatial mesh elements. Well-posedness of the fully discrete scheme and error analysis will be shown. For a time interval (0, T) and a spatial domain Ω, our analysis suggest that the error in \(L^{2}\left ((0,T),L^{2}({\Omega })\right )\)-norm is \(O(k^{2-\frac {\mu }{2}}+h^{2})\) (that is, short by order \(\frac {\mu }{2}\) from being optimal in time) where k denotes the maximum time step, and h is the maximum diameter of the elements of the (quasi-uniform) spatial mesh. However, our numerical experiments indicate optimal O(k² + h²) error bound in the stronger \(L^{\infty }\left ((0,T),L^{2}({\Omega })\right )\)-norm. Variable time steps are used to compensate the singularity of the continuous solution near t = 0.