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The structure, tautomeric preferences, base-pairing ability, stacking interactions and HOMO-LUMO gaps of the naphtho-homologated DNA bases are studied using theoretical techniques. The bases have structures similar to the benzo-fused predecessors and show a tautomeric preference to naphtho-thymine and naphtho-adenine resulting in formation of hydrogen-bonded dimers.

The effect of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is studied. The results reveal notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding.

The results from investigation of the electronic properties of an xDNA duplex made of natural and benzo-homologated bases and a natural one with an analogous sequence suggest that xDNA has a smaller [pi]-[pi]* gap than B-DNA suggests and could be used as plausible candidate for molecular-wire applications.

A comprehensive ab initio study is used to observe and analyze the structure, stability and electronic properties of guanine-zinc-cytosine (G-Zn-C) base pair, which when combined with metals like Zn and Co lead to the formation of M-DNA at high values of pH. The analysis suggest that a lot of things should be taken care of while studying the electronic properties of such base-pairs, as M-DNAs with functionals do not account for strong electronic correlations.

Second-order Moller-Plesset perturbation theory and density functional theory (DFT) are used to investigate the structural and electronic properties of size-expanded DNA bases, xA, xC, xG, and xT, and their natural counterparts. The results show that natural and size-expanded bases have both nonplanar amino groups, but the latter also has nonplanar aromatic rings, and xG is easier to oxidize than G.

Ionophore antibiotics (IPAs) are polyether compounds used in broiler feed to promote growth and control coccidiosis. Most of the ingested IPAs are excreted into broiler litter (BL), a mixture of excreta and bedding material. BL is considered a major source of IPAs released into the environment as BL is commonly used to fertilize agricultural fields. This study investigated IPA biodegradation in BL and soil microcosms, as a process affecting the fate of IPAs in the environment. The study focused on the most widely used IPAs, monensin (MON), salinomycin (SAL), and narasin (NAR). MON was stable in BL microcosms at 24-72% water content (water/wet litter, w/w) and 35-60 °C, whereas SAL and NAR degraded under certain conditions. Factor analysis was conducted to delineate the interaction of water and temperature on SAL and NAR degradation in the BL. A major transformation product of SAL and NAR was identified. Abiotic reaction(s) were primarily responsible for the degradation of MON and SAL in nonfertilized soil microcosms, whereas biodegradation contributed significantly in BL-fertilized soil microcosms. SAL biotransformation in soil microcosms yielded the same product as in the BL microcosms. A new primary biotransformation product of MON was identified in soil microcosms. A field study showed that MON and SAL were stable during BL stacking, whereas MON degraded after BL was applied to grassland. The biotransformation product of MON was also detected in the top soil layer where BL was applied. [ABSTRACT FROM AUTHOR]

Healthy Wistar rats were supplemented during 20 weeks with commercial inulin (I) and Agave tequilana fructans (CAT), experimental fructans from A. tequilana (EAT) and A. salmiana (AS) mature stems, rice starch 10% (RS), and standard feed for rodents (C). Feed intake was kept steady, but with I, body weight and abdominal adipose tissue (6.01 g) decreased at the end. Glucose (mg/dL) (C, 120.52; I, 110.69; CAT, 105.75; EAT, 115.48; AS, 101.63; and RS, 121.82), total cholesterol (C, 89.89; I, 64.48; CAT, 68.04; EAT, 68.74; AS, 68.04; and RS, 82), and triglycerides (C, 84.03; I, 59.52; CAT, 68.56; EAT, 59.08; AS, 75.27; and RS, 81.8) kept being normal and without differences between fructans. At the end, there was a significant increase in lactic acid bacteria when the I and AS groups were compared to the C group (C, 9.18; I, 10.64; CAT, 10.34; EAT, 10.36; AS, 10.49; and RS, 9.62 log 10 CFU/g of feces). In addition, with fructans, there was an accelerated process in feces emptiness, Lieberkühn crypts kept their morphology, and there was an increment of goblet cells., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

The physisorbed (precursor) and chemisorbed states of a molecule on metal surfaces can be utilized to build a logic switch at the single-molecule level, enabling further microminiaturization of electronic devices beyond the silicon limits. However, a serious drawback of this design is easy lateral diffusion of the molecule in the physisorbed state, which may destroy the normal switch operation. Here, we demonstrate that anchoring engineering can be an effective way to enhance the stability of molecular switches without degrading switching functionality. As exemplified by trans-ADT on Cu(111), we show that the lateral diffusion of such molecular switch can be obstructed by the anchoring of the ending thiophene groups, along with a rotation of the adsorbate during the switching process. More general, our results also suggest that when searching for molecular switches with reversible physisorbed and chemisorbed states with excellent bistability and lateral stability, the focus should be on finding molecules with a moderate HOMO-LUMO energy gap and anchoring atoms with positive charge that can then be deposited on substrates with which they interact moderately. This allows further improvement of the lateral and vertical stability of such a molecular switch by substituting the thiophene groups with selenophene, thus establishing trans-ADS on Cu(111) as a promising switch.

Conductivity of two-dimenstional (2D) materials, which largely determines the efficiency and reliability of nanodevices, is proportional to the product of carrier concentration and mobility. Conventional doping, such as ionic substitution or introduction of vacancies, increases carrier concentration and decreases carrier mobility due to the scattering or trapping of carriers. We propose a remote-doping strategy that enables the simultaneous enhancement of both parameters. Density functional theory calculations in 2D InSe reveal that adsorbing the molecule tetrathiafulvalene (TTF) and applying a 4% external tensile strain leads to an increase in the carrier concentration of the TTF-InSe system that is 13 orders of magnitude higher than that of the pristine counterpart, whereas the carrier mobility is enhanced by 35% compared with the InSe monolayer. As a consequence of the synergetic role of molecule doping and strain engineering, ultrahigh conductivity of 1.85 × 10 5 S/m is achieved in the TTF-InSe system at room temperature.

Bacterial microcompartments, BMCs, are organelles that exist within wide variety of bacteria and act as nanofactories. Among the different types of known BMCs, the carboxysome has been studied the most. The carboxysome plays an important role in the light-independent part of the photosynthesis process, where its icosahedral-like proteinaceous shell acts as a membrane that controls the transport of metabolites. Although a structural model exists for the carboxysome shell, it remains largely unknown how the shell proteins self-assemble. Understanding the self-assembly process can provide insights into how the shell affects the carboxysome's function and how it can be modified to create new functionalities, such as artificial nanoreactors and artificial protein membranes. Here, we describe a theoretical framework that employs Monte Carlo simulations with a coarse-grain potential that reproduces well the atomistic potential of mean force; employing this framework, we are able to capture the initial stages of the 2D self-assembly of CcmK2 hexamers, a major protein-shell component of the carboxysome's facet. The simulations reveal that CcmK2 hexamers self-assemble into clusters that resemble what was seen experimentally in 2D layers. Further analysis of the simulation results suggests that the 2D self-assembly of carboxysome's facets is driven by a nucleation-growth process, which in turn could play an important role in the hierarchical self-assembly of BMC shells in general.

Ionophore antibiotics (IPAs) are polyether compounds used in broiler feed to promote growth and control coccidiosis. Most of the ingested IPAs are excreted into broiler litter (BL), a mixture of excreta and bedding material. BL is considered a major source of IPAs released into the environment as BL is commonly used to fertilize agricultural fields. This study investigated IPA biodegradation in BL and soil microcosms, as a process affecting the fate of IPAs in the environment. The study focused on the most widely used IPAs, monensin (MON), salinomycin (SAL), and narasin (NAR). MON was stable in BL microcosms at 24-72% water content (water/wet litter, w/w) and 35-60 °C, whereas SAL and NAR degraded under certain conditions. Factor analysis was conducted to delineate the interaction of water and temperature on SAL and NAR degradation in the BL. A major transformation product of SAL and NAR was identified. Abiotic reaction(s) were primarily responsible for the degradation of MON and SAL in nonfertilized soil microcosms, whereas biodegradation contributed significantly in BL-fertilized soil microcosms. SAL biotransformation in soil microcosms yielded the same product as in the BL microcosms. A new primary biotransformation product of MON was identified in soil microcosms. A field study showed that MON and SAL were stable during BL stacking, whereas MON degraded after BL was applied to grassland. The biotransformation product of MON was also detected in the top soil layer where BL was applied.

We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.

Self-assembled monolayers are the basis for molecular nanodevices, flexible surface functionalization, and dip-pen nanolithography. Yet self-assembled monolayers are typically created by a rather inefficient process involving thermally driven attachment reactions of precursor molecules to a metal surface, followed by a slow and defect-prone molecular reorganization. Here we demonstrate a nonthermal, electron-induced approach to the self-assembly of phenylacetylene molecules on gold that allows for a previously unachievable attachment of the molecules to the surface through the alkyne group. While thermal excitation can only desorb the parent molecule due to prohibitively high activation barriers for attachment reactions, localized injection of hot electrons or holes not only overcomes this barrier but also enables an unprecedented control over the size and shape of the self-assembly, defect structures, and the reverse process of molecular disassembly from a single molecule to a mesoscopic length scale. Electron-induced excitation may therefore enable new and highly controlled approaches to molecular self-assembly on a surface.

We consider nanometer-sized fluid annuli (rings) deposited on a solid substrate and ask whether these rings break up into droplets due to the instability of Rayleigh-Plateau-type modified by the presence of the substrate, or collapse to a central drop due to the presence of azimuthal curvature. The analysis is carried out by a combination of atomistic molecular dynamics simulations and a continuum model based on a long-wave limit of Navier-Stokes equations. We find consistent results between the two approaches, and demonstrate characteristic dimension regimes which dictate the assembly dynamics.

Supramolecular self-assembly on well-defined surfaces provides access to a multitude of nanoscale architectures, including clusters of distinct symmetry and size. The driving forces underlying supramolecular structures generally involve both graphoepitaxy and weak directional nonconvalent interactions. Here we show that functionalizing a benzene molecule with an ethyne group introduces attractive interactions in a 2D geometry, which would otherwise be dominated by intermolecular repulsion. Furthermore, the attractive interactions enable supramolecular self-assembly, wherein a subtle balance between very weak CH/π bonding and molecule-surface interactions produces a well-defined "magic" dimension and chirality of supramolecular clusters. The nature of the process is corroborated by extensive scanning tunneling microscopy/spectroscopy (STM/S) measurements and ab initio calculations, which emphasize the cooperative, multicenter characters of the CH/π interaction. This work points out new possibilities for chemical functionalization of π-conjugated hydrocarbon molecules that may allow for the rational design of supramolecular clusters with a desired shape and size., (© 2011 American Chemical Society)

Controlling the movement of nanoscale objects is a significant goal of nanotechnology. Dewetting-induced ejection of nanodroplets could provide another means of achieving that goal. Molecular dynamics simulations were used to investigate the dewetting-induced ejection of nanoscale liquid copper nanostructures that were deposited on a graphitic substrate. Nanostructures in the shape of a circle, square, equilateral, and isosceles triangle dewet and form nanodroplets that are ejected from the substrate with a velocity that depends on the initial shape and temperature. The dependence of the ejected velocity on shape is ascribed to the temporal asymmetry of the mass coalescence during the droplet formation; the dependence on temperature is ascribed to changes in the density and viscosity. The results suggest that dewetting induced by nanosecond laser pulses could be used to control the velocity of ejected nanodroplets., (© 2011 American Chemical Society)

Quantum mechanical (QM) calculations, classical grand canonical Monte Carlo (GCMC) simulations, and classical molecular dynamics (MD) simulations are performed to test the effect of charge distribution on hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) adsorption and diffusion in IRMOF-10. Several different methods for mapping QM electron distributions onto atomic point charges are explored, including the electrostatic potential (ESP) method, Mulliken population analysis, Lowdin population analysis, and natural bond orbital analysis. Classical GCMC and MD simulations of RDX in IRMOF-10 are performed using 15 combinations of charge sources of RDX and IRMOF-10. As the charge distributions vary, interaction potential energies, the adsorption loading, and the self-diffusivities are significantly different. None of the 15 combinations are able to quantitatively capture the dependence of the energy of adsorption on local configuration of RDX as observed in the QM calculations. We observe changes in the charge distributions of RDX and IRMOF-10 with the introduction of an RDX molecule into the cage. We also observe a large dispersion contribution to the interaction energy from QM calculations that is not reproduced in the classical simulations, indicating that the source of discrepancy may not lie exclusively with the assignment of charges.

We have demonstrated in our earlier work that a few natural and synthetic estrogens can be effectively transformed through reactions mediated by lignin peroxidase (LiP). The behaviors of such reactions are variously influenced by the presence of natural organic matter (NOM) and/or veratryl alcohol (VA). Certain white rot fungi, e.g. Phanerochaete chrysosporium, produce VA as a secondary metabolite along with LiP in nature where NOM is ubiquitously present. Herein, we report a study on the products resulting from LiP-mediated oxidative coupling reactions of a representative estrogen, 17beta-estradiol (E2), and how the presence of NOM and/or VA impacts the formation and distribution of the products. A total of six products were found, and the major products appeared to be oligomers resulting from E2 coupling. Our experiments revealed that these products likely formed colloidal solids in water that can be removed via ultrafiltration or settled during ultracentrifugation. Such a colloidal nature of the products could have important implications in their treatability and environmental transport. In the presence of VA, the products tended to shift toward higher-degree of oligomers. When NOM was included in the reaction system, cross-coupling between E2 and NOM appeared to occur. Data obtained from E-SCREEN test confirmed that the estrogenicity of E2 can be effectively eliminated following sequential reactions mediated by LiP.

The influence of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is examined. To this end, the local aromaticity of the six- and five-membered rings in both the natural bases and their benzoderivatives is determined using HOMA, NICS, aromatic fluctuation index (FLU), and para-delocalization index (PDI) descriptors. In general, there is a good correspondence between the different indices, so that ring moieties with more negative NICS values also have larger HOMA and PDI measures and lower FLU indices. The results also point out notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding. The differences in the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap determined for the size-expanded nucleobases show an inverse correlation with the aromaticity of the fused benzene ring, so that the larger the HOMO-LUMO gap is, the lower the destabilization experienced by the benzene upon insertion/addition to the natural bases. This finding suggests that the introduction of suitable chemical modifications in the benzene ring might be useful to modulate the HOMO-LUMO gap while enabling the design of modified DNA duplexes that are able to act as molecular wires.

A novel approach to molecular negentropy from the point of view of Markov models is introduced. Stochastic negentropies (MEDNEs) are used to develop a linear discriminant analysis. The discriminant analysis produced a set of two discriminant functions, which gave rise to a very good separation of 93.38% of 151 chemicals (training series) into two groups. The total predictability (86.67%, i.e., 52 compounds out of 60) was tested by means of an external validation set. Randić's orthogonalization procedures allowed interpretation of the model while avoiding collinearity descriptors. On the other hand, factor analysis was used to suggest the relation of MEDNEs with other molecular descriptors and properties into a property space. Three principal factors (related to three orthogonal MEDNEs) can be used to explain approximately 90% of the variance of different molecular parameters of halobenzenes including bulk, energetic, dipolar, molecular surface-related, and hydrophobic parameters. Finally, preliminary experimental results coincide with a theoretical prediction when agranulocytosis induction by G-1, a novel microcidal that presents Z/E isomerism, is not detected.

A new application of TOPological Sub-structural MOlecular DEsign (TOPS-MODE) was carried out in herbicides using computer-aided molecular design. Two series of compounds, one containing herbicide and the other containing nonherbicide compounds, were processed by a k-Means Cluster Analysis in order to design the training and prediction sets. A linear classification function to discriminate the herbicides from the nonherbicide compounds was developed. The model correctly and clearly classified 88% of active and 94% of inactive compounds in the training set. More specifically, the model showed a good global classification of 91%, i.e., (168 cases out of 185). While in the prediction set, they showed an overall predictability of 91% and 92% for active and inactive compounds, being the global percentage of good classification of 92%. To assess the range of model applicability, a virtual screening of structurally heterogeneous series of herbicidal compounds was carried out. Two hundred eighty-four out of 332 were correctly classified (86%). Furthermore this paper describes a fragment analysis in order to determine the contribution of several fragments toward herbicidal property; also the present of halogens in the selected fragments were analyzed. It seems that the present TOPS-MODE based QSAR is the first alternate general "in silico" technique to experimentation in herbicides discovery.