Two-membered Ring Research Articles

Mft1, identified from a genome-wide screen of the yeast haploid mutants, mediates cell cycle arrest to counteract quinoxaline-induced toxicity.

Quinoxaline is a heterocyclic compound with a two-membered ring structure that undergoes redox cycling to produce toxic free radicals. It has antiviral, antibacterial, antifungal, and antitumor activities. However, the biological functions that are involved in mounting a response against the toxic effects of quinoxaline have not been investigated. Herein, we performed a genome-wide screen using the yeast haploid mutant collection and reported the identification of 12 mutants that displayed varying sensitivity towards quinoxaline. No mutant was recovered that showed resistance to quinoxaline. The quinoxaline-sensitive mutants were deleted for genes that encode cell cycle function, as well as genes that belong to other physiological pathways such as the vacuolar detoxification process. Three of the highly sensitive gene-deletion mutants lack the DDC1, DUN1, and MFT1 genes. While Ddc1 and Dun1 are known to perform roles in the cell cycle arrest pathway, the role of Mft1 remains unclear. We show that the mft1Δ mutant is as sensitive to quinoxaline as the ddc1Δ mutant. However, the double mutant ddc1Δ mft1Δ lacking the DDC1 and MFT1 genes, is extremely sensitive to quinoxaline, as compared to the ddc1Δ and mft1Δ single mutants. We further show that the mft1Δ mutant is unable to arrest in the G2/M phase in response to the drug. We conclude that Mft1 performs a unique function independent of Ddc1 in the cell cycle arrest pathway in response to quinoxaline exposure. This is the first demonstration that quinoxaline exerts its toxic effect likely by inducing oxidative DNA damage causing cell cycle arrest. We suggest that clinical applications of quinoxaline and its derivatives should entail targeting cancer cells with defective cell cycle arrest.

Periodic modeling of zeolite Ti-LTA.

We have proposed a combination of density functional theory calculations and interatomic potential-based simulations to study the structural, electronic, and mechanical properties of pure-silica zeolite Linde Type A (LTA), as well as two titanium-doped compositions. The energetics of the titanium distribution within the zeolite framework suggest that the inclusion of a second titanium atom with configurations Ti-(Si)0-Ti, Ti-(Si)1-Ti, and Ti-(Si)2-Ti is more energetically favorable than the mono-substitution. Infra-red spectra have been simulated for the pure-silica LTA, the single titanium substitution, and the configurations Ti-(Si)0-Ti and Ti-(Si)2-Ti, comparing against experimental benchmarks where available. The energetics of the direct dissociation of water on these Lewis acid sites indicate that this process is only favored when two titanium atoms form a two-membered ring (2MR) sharing two hydroxy groups, Ti-(OH)2-Ti, which suggests that the presence of water may tune the distribution of titanium atoms within the framework of zeolite LTA. The electronic analysis indicates charge transfer from H2O to the Lewis acid site and hybridization of their electronic states.

Water Interactions with Nanoporous Silica: Comparison of ReaxFF and ab Initio based Molecular Dynamics Simulations

Detailed understanding of the reactions and processes which govern silicate–water interactions is critical to geological, materials, and environmental sciences. Interactions between water and nanoporous silica were studied using classical molecular dynamics with a Reactive Force Field (ReaxFF), and the results were compared with density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations. Two versions of ReaxFF Si/O/H parametrizations (Yeon et al. J. Phys. Chem. C 2016, 120, 305 and Fogarty et al. J. Chem. Phys. 2010, 132, 174704) were compared with AIMD results to identify differences in local structures, water dissociation mechanisms, energy barriers, and diffusion behaviors. Results identified reaction mechanisms consisting of two different intermediate structures involved in the removal of high energy two-membered ring (2-Ring) defects on complex nanoporous silica surfaces. Intermediate defects lifetimes affect hydroxylation and 2-Ring defect removal. Additionally, the limite...

Thermochemistry of N-heterocyclic carbenes with 5-, 4-, 3-, and 2-membered rings

N-heterocyclic carbenes (NHCs) based on imidazole-2-ylidene (1) or the saturated imidazolidine-2-ylidene (2) scaffolds are long-lived singlet carbenes. Both benefit from inductive stabilization of the sigma lone pair on carbon by neighboring N atoms and delocalization of the N pi lone pairs into the nominally vacant p-pi atomic orbital at the carbene carbon. With thermochemical schemes G4 and CBS-QB3, we estimate the relative thermodynamic stabilization of smaller ring carbenes and acyclic species which may share the keys to NHC stability. These include four-membered ring systems incorporating the carbene center, two trivalent N centers, and either a boron or a phosphorus atom to complete the ring. Amino-substituted cyclopropenylidenes have been reported but three-membered rings containing the carbene center and two N atoms are not known. Our calculations suggest that amino-substituted cyclopropenylidenes are comparable in stability to the four-membered NHCs but that diazacyclopropanylidenes would be substantially less effectively stabilized. Concluding the series are acyclic carbenes with and without neighboring N atoms and a series of two-membered ring azapropadienenylidene cations of form :CNW with W = an electron-withdrawing agent. We have studied W = NO2, CH2(+), CF2(+), and (CN)(2)C(+). Although these systems display a degree of stabilization and carbene-like electronic structure, the stability of the NHCs is unsurpassed. (c) 2014 Wiley Periodicals, Inc.

A DFT study on the hydrolysis stabilities of silica molecular chains and rings based on the two-membered rings

The reactivity of silica toward to water is an important issue in environmental science and materials science for many years. In this paper, we study the hydrolysis stabilities of silica molecular chains and molecular rings based on two-membered silica ring by performing density functional theory calculations. It is found that the hydrolysis for the linear molecular chains firstly takes place in the middle parts and carries on gradually to the ends. In contrast with the early conjecture that the molecular rings might have higher hydrolysis stability than the corresponding linear chains, we find that these fully coordinated molecular rings are less stable than the corresponding molecular chains with the presence of water molecule.

Structures and Properties of Silicon Oxide Clusters by Theoretical Investigations

In this paper, we outline our computational work in the area of silicon oxide clusters. To reduce the computational cost, we designed an economic basis set for silicon oxide systems, and reliable structures were obtained by this approach. To reveal the formation mechanism of silicon nanowires, we investigated the structures and properties of silicon suboxide clusters in particular monoxide clusters that play an important role in the oxide-assisted growth. And to improve our understanding of the silicon dioxide clusters and to bridge the gap between gas phase and solid phase silica, we proposed several models based on the two-membered ring (2MR), three-membered ring (3MR), four-membered ring (4MR), the hybrid of the 2MR and 3MR, or the 3MR and 4MR.

Silica Nanoarchitectures with Tailored Pores Based on the Hybrid Three- and Four-Membered Rings

Inspired by the recent developments in the controlled synthesis of porous materials, we present herein the structural prediction of silica nanoarchitectures by using the three- (3MRs) and four-membered rings (4MRs), which are more frequently found in the nanometer-sized particles than in the bulk form, as building blocks. The proposed models include the active molecular rings, thin nanowires, hollow nanotubes, discrete fullerene-like cages, and porous zeolite-like three-dimensional networks. Their geometrical and electronic structures and properties were studied by performing density functional calculations. These silica nanostructures were proved, using molecular dynamics simulations, to possess intrinsic structural stabilities with highly symmetrical geometries and regular nanochannels. These atomically well-defined clusters, (SiO)(n), are chemically more reactive than those proposed earlier and are energetically more favorable for n > 20 in high-level density functional calculations over the corresponding two-membered ring (2MR) chains and rings as well as the pure 3MR networks. The nanoparticles and nanodevices based on them are expected to have potential technological applications that mainly make use of their characteristic geometrical structures (nanosized pores) and novel electronic properties.

Stability and Size Effect of Silica Nanotube

Abstract The structure and infrared vibration of silica nanotubes with anhydrous structure (SiO 2-NTs) and hydrogen-capped structure (SiO 2-WNTs) were investigated using density-functional theory (DFT). It was found that the average binding energy was all the same for SiO 2-WNTs with the same layer number or length. SiO 2-WNTs were energetically more favorable than the SiO 2-NTs and two-membered ring (2MR) molecular chains structure. The IR spectrum of 4MR-WNTs was in well accord with the experimental data, and the vibrations of oxygen atoms, which were in directions parallel or normal to the axis of nanotubes, showed a strong size effect. The results indicated that SiO 2-WNTs is an appropriate structure model for one-dimensional silica nanotube.

Calculation of structure and properties of one-dimensional silica nanomaterials based on first-principle

We have studied silica single and double chain based on two-membered ring and nanotubes based on three-membered ring using the density-functional theory at 6-31G(d) level. The average binding energy, electronic structure and vibration frequency were calculated. Our calculations show that the average binding energy and energy gap monotonically change with increasing SiO2 units. Infrared spectrum indicated that the frequency and intensity of radial and tangential vibration shift obviously. Radial vibration frequency shifts to high frequency while tangential vibration frequency shifts to low frequency showing the existence of quantum size effect and anisotropic property of vibration in SiO2 nanomaterial.

Structural Model of Silica Nanowire Assembled from a Highly Stable (SiO2)8 Unit

The ground-state structures of silica clusters (SiO2)n for n = 1-8 were studied by performing calculations at the B3LYP/6-311+G(d) level of density functional theory. The results indicate that the growth mode of a silica nanowire based on small silica clusters may change at different wire lengths. A linear chain might be assembled from the smallest clusters of rhombic two-membered ring (2MR) with n < or = 5, while the growth motif changes at n = 6 into a more compact form composed of three-membered-rings (3MRs). The 3MR-containing structures become energetically favorable configurations for even longer silica clusters. In particular, the closed molecular ring consisting of 3MRs at n = 8 (i.e., (SiO2)8) with a high symmetry shows extreme energetic stability and relatively high chemical reactivity and thus is considered to be an important building block to assemble into silica nanowires. The relative stability of so-assembled silica nanowires were evaluated and compared with the models of silica nanowires in the literature.

Water adsorption on amorphous silica surfaces: a Car–Parrinello simulation study

A combination of classical molecular dynamics (MD) and ab initio Car–Parrinellomolecular dynamics (CPMD) simulations is used to investigate the adsorptionof water on a free amorphous silica surface. From the classical MD,SiO2 configurations with a free surface are generated which are then used as starting configurations for theCPMD. We study the reaction of a water molecule with a two-membered ring at the temperatureT = 300 K. We show that the result of this reaction is the formation of two silanol groups on thesurface. The activation energy of the reaction is estimated and it is shown that the reactionis exothermic.

O Triclusters Revisited: Classical MD and Quantum Cluster Results for Glasses of Composition (Al2O3)2(SiO2).

The (17)O NMR spectrum of CaAl(2)Si(2)O(8) glass shows two types of O sites that are not present in the crystalline material. One of these, with (17)O NMR parameters C(Q) = 2.3 MHz and delta = +20 ppm, has been assigned to a O, a local geometry in which the O is coordinated to three tetrahedrally coordinated atoms, either Al or Si. For crystalline CaAl(4)O(7), a tricluster site (with three Al linkages to O, i.e., OAl(3)) has been characterized experimentally, with a C(Q) of 2.5 MHz and a delta of about +40 ppm. Thus, a C(Q) value of 2.5 MHz or less seems to be a characteristic of such sites, although they may show a range of delta values. However, several different quantum chemical cluster calculations employing energy-optimized geometries for various tricluster species have given C(Q) values considerably larger than that seen experimentally in the CaAl(2)Si(2)O(8) glass (with minimum C(Q) values of 3.0 MHz even for all Al species). We have recently shown that for edge-sharing geometries, in which the tricluster O atoms participate in of composition Al(2)O(2), the calculated C(Q) values are considerably lower, in the range identified in the glass. However, such two-membered ring geometries had been observed only in crystalline inorganic alumoxanes. Ab initio MD calculations on related compositions, such as the calcium aluminosilicate, CAS, (CaO)(0.21)(Al(2)O(3))(0.12)(SiO(2))(0.67), show a small percentage of O triclusters, but none in two-membered rings of the Al(2)O(2) type, and the calculated C(Q) values for the triclusters that do exist are higher than seen in the original experiments on CaAl(2)Si(2)O(8) glass and not significantly different from those for two-coordinate O in Si-O-Al sites. However, a classical MD simulation of the structure of glassy aluminum silicate AS2, (Al(2)O(3))2(SiO(2)), gave a predominance of O triclusters within two-membered rings, with structures much like those seen in the alumoxanes. We have now calculated (17)O nuclear quadrupole coupling constants and NMR shielding values for clusters extracted from these simulations, using standard quantum chemical methods. The calculated C(Q) values for these O triclusters are now in the range observed experimentally in the CaAl(2)Si(2)O(8) glass (around 2.3-2.6 MHz) when the tricluster O is surrounded by three Al, two of which are part of an Al(2)O(2) ring. This supports the experimentalists' contention that such tricluster O species do exist and have been seen by (17)O NMR.

O Triclusters Revisited: Classical MD and Quantum Cluster Results for Glasses of Composition (Al2O3)2(SiO2)

The (17)O NMR spectrum of CaAl(2)Si(2)O(8) glass shows two types of O sites that are not present in the crystalline material. One of these, with (17)O NMR parameters C(Q) = 2.3 MHz and delta = +20 ppm, has been assigned to a "tricluster" O, a local geometry in which the O is coordinated to three tetrahedrally coordinated atoms, either Al or Si. For crystalline CaAl(4)O(7), a tricluster site (with three Al linkages to O, i.e., OAl(3)) has been characterized experimentally, with a C(Q) of 2.5 MHz and a delta of about +40 ppm. Thus, a C(Q) value of 2.5 MHz or less seems to be a characteristic of such sites, although they may show a range of delta values. However, several different quantum chemical cluster calculations employing energy-optimized geometries for various tricluster species have given C(Q) values considerably larger than that seen experimentally in the CaAl(2)Si(2)O(8) glass (with minimum C(Q) values of 3.0 MHz even for all Al species). We have recently shown that for edge-sharing geometries, in which the tricluster O atoms participate in "two-membered rings" of composition Al(2)O(2), the calculated C(Q) values are considerably lower, in the range identified in the glass. However, such two-membered ring geometries had been observed only in crystalline inorganic alumoxanes. Ab initio MD calculations on related compositions, such as the calcium aluminosilicate, CAS, (CaO)(0.21)(Al(2)O(3))(0.12)(SiO(2))(0.67), show a small percentage of O triclusters, but none in two-membered rings of the Al(2)O(2) type, and the calculated C(Q) values for the triclusters that do exist are higher than seen in the original experiments on CaAl(2)Si(2)O(8) glass and not significantly different from those for two-coordinate O in Si-O-Al sites. However, a classical MD simulation of the structure of glassy aluminum silicate AS2, (Al(2)O(3))2(SiO(2)), gave a predominance of O triclusters within two-membered rings, with structures much like those seen in the alumoxanes. We have now calculated (17)O nuclear quadrupole coupling constants and NMR shielding values for clusters extracted from these simulations, using standard quantum chemical methods. The calculated C(Q) values for these O triclusters are now in the range observed experimentally in the CaAl(2)Si(2)O(8) glass (around 2.3-2.6 MHz) when the tricluster O is surrounded by three Al, two of which are part of an Al(2)O(2) ring. This supports the experimentalists' contention that such tricluster O species do exist and have been seen by (17)O NMR.

A structural model of one-dimensional thin silica nanowires

We report a new structural model of silica molecular wire based on spiro union two-membered ring (SU-2MR) units. As revealed by density functional calculations, the SU-2MR wire is formed by parallel 2MRs bridged by oxygen atoms and is energetically more favorable, thermally more stable and chemically more reactive at the tip than the edge-sharing two-membered ring molecular chain proposed early. The SU-2MR molecular chain would be considered as an appropriate structural model of one-dimensional thin (0.4 nm) silica nanowires.

Adsorption and vibrational spectroscopy of ammonia at mordenite: ab initio study.

The adsorption of ammonia at various active centers at the outer and inner surfaces of mordenite, involving Brønsted acid (BA) sites, terminal silanol groups, and Lewis sites has been investigated using periodic ab initio density-functional theory. It is shown that ammonia forms an ammonium ion when adsorbed at strong BA sites. The calculated adsorption energies for different BA sites vary in the interval from 111.5 to 174.7 kJ/mol depending on the local environment of the adduct. The lowest adsorption energy is found for a monodentate complex in the main channel, the highest for a tetradentate configuration in the side pocket. At weak BA sites such as terminal silanol groups or a defect with a BA site in a two-membered ring ammonia is H bonded via the N atom. Additional weak H bonds are formed between H atoms of ammonia and O atoms of neighboring terminal silanol groups. The calculated adsorption energies for such adducts range between 61.7 and 70.9 kJ/mol. The interaction of ammonia with different Lewis sites is shown to range between weak (DeltaE(ads)=17.8 kJ/mol) and very strong (DeltaE(ads)=161.7 kJ/mol), the strongest Lewis site being a tricoordinated Al atom at the outer surface. Our results are in very good agreement with the distribution of desorption energies estimated from temperature-programmed desorption (TPD) and microcalorimetry experiments, the multipeaked structure of the TPD spectra is shown to arise from strong and weak Brønsted and Lewis sites. The vibrational properties of the adsorption complexes are investigated using a force-constant approach. The stretching and bending modes of NH(4) (+) adsorbed to the zeolite are strongly influenced by the local environment. The strongest redshift is calculated for the asymmetric stretching mode involving the NH group hydrogen bonded to the bridging O atom of the BA site, the shift is largest for a monodentate and smallest for a tetradentate adsorption complex. The reduced symmetry of the adsorbate also leads to a substantial splitting of the stretching and bending modes. In agreement with experiment we show that the main vibrational feature which differentiates coordinatively bonded ammonia from a hydrogen-bonded ammonium ion is the absence of bending modes above 1630 cm(-1) and in the region between 1260 and 1600 cm(-1), and a low-frequency bending band in the range from 1130 to 1260 cm(-1). The calculated distribution of vibrational frequencies agrees very well with the measured infrared adsorption spectra. From the comparison of the adsorption data and the vibrational spectra we conclude that due to the complex adsorption geometry the redshift of the asymmetric stretching is a better measure of the acidity of an active sites than the adsorption energy.

Hydrolysis of a two-membered silica ring on the amorphous silica surface.

We have combined density functional theory (DFT) with classical interatomic potential functions to model hydrolysis of amorphous silica surfaces. The water-silica interaction is described by DFT with incorporation of a long-range elastic field described by classical interatomic potentials. Both physisorption and chemisorption of water on a surface site, known as the two-membered silica ring, are studied in detail. The hybrid quantum-mechanical and classical mechanical method enables more realistic treatment of chemical processes on an extended surface than previous methods. We have studied cooperative events in the hydrolytic reactions and discovered a new reaction pathway that involves a double proton transfer process. In addition, the evaluation of the total energy in a hybrid quantum-mechanical and classical mechanical system is discussed.

Water–silica surface interactions: A combined quantum-classical molecular dynamic study of energetics and reaction pathways

We report studies of water–silica surface interactions using a hybrid first-principles–classical molecular dynamics simulation method. The quantum region, which is treated with high accuracy density functional theory, is embedded in a large amorphous matrix described by classical potentials. With this model, both nondissociative and dissociative processes of water molecules at a two-membered ring site, which has been found experimentally on the surface, are studied. Our investigations provide qualitative and quantitative descriptions of the reaction pathways and energy landscape. A barrier-free double hydrogen atom transfer process is observed.

Defect sites at the (001) surface of mordenite: An ab initio study

The mechanisms and energetics of the formation of various defects upon dehydration of the surface of pure-siliceous and Al-monosubstituted mordenite are investigated using a periodic ab initio density functional theory technique. An energetically favorable defect at the pure-siliceous surface is a strained two-membered Si–O ring (2MR) formed via elimination of a water molecule from a pair of neighboring terminal silanol groups. Assuming the formation of two-membered rings, the dehydration-energy of the (001) surface of pure-silica mordenite is 133 kJ/mol. A relatively high reaction barrier of 179 kJ/mol coincides with the experimental observation that these defects are formed at high temperatures &amp;gt;700 K. Despite a short Si–Si distance of 2.35 Å across the 2MR which is comparable to the bond length between Si atoms in silicon in diamond structure, the electron-localization function reveals no bonding interaction between Si atoms on the 2MR. In the Al-substituted surfaces, the dehydration proceeds via proton transfer from the Brønsted-acid site (BA) to a neighboring terminal hydroxyl group. The low values of two subsequent energetic barriers of dehydration of 13 and 10 kJ/mol suggest that the surface BA sites are likely to be destroyed at even modest temperatures. The most stable defects formed in this mechanism are ones containing a threefold-coordinated Al atom and a defect with both an Al atom and a bridging OH group located on a two-membered ring. The heat of reaction of only 9 kJ/mol and the activation energy of the transformation between these two configurations of 26 kJ/mol suggest that both defects occur with similar probability.