Effect of the Orientational Disorder on the Observed Geometry of Carboxylic Group in Dimers of Carboxylic Acids in Crystalline State

Joint considerations of twofold symmetry axes producing various orientations of carboxylic groups and of non-coplanarity of these groups in a dimer lead to a new classification of orientational disorder in crystal s of cyclic dimers of carboxylic acids. Analysis of the geometry and particularly of the anisotropic thermal parameters of carboxylic atoms allows one to distinguish between the possible types of orientational disorder. Influences of dynamic disorder and mesomeric effects are discussed as well

Environment influences on the aromatic character of nucleobases and amino acids

Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues

Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO2, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO2 or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO2) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question

Bis­(μ-pyridine-2,3-dicarboxyl­ato)bis­[aqua­(3-carb­oxy­pyridine-2-carboxyl­ato)indium(III)] tetra­hydrate

In the binuclear centrosymmetric title compound, [In2(C7H3NO4)2(C7H4NO4)2(H2O)2]·4H2O, which contains both pyridine-2,3-dicarboxyl­ate and 3-carb­oxy­pyridine-2-carboxyl­ate ligands, the InIII atom is six-coordinated in a distorted octa­hedral geometry. One pyridine ligand is N,O-chelated while the other is N,O-chelated and at the same time bridging to the other via the second carboxyl group. In the crystal, an extensive O—H⋯O hydrogen-bonding network, involving the coordinated and lattice water mol­ecules and the carboxyl groups of the ligands, together with C—H⋯O and π–π inter­actions [centroid–centroid distance = 3.793 (1) Å], leads to the formation of a three-dimensional structure

Electron-topological, energetic and π-electron delocalization analysis of ketoenamine-enolimine tautomeric equilibrium

The ketoenamine-enolimine tautometic equilibrium has been studied by the analysis of aromaticity and electron-topological parameters. The influence of substituents on the energy of the transition state and of the tautomeric forms has been investigated for different positions of chelate chain. The quantum theory of atoms in molecules method (QTAIM) has been applied to study changes in the electron-topological parameters of the molecule with respect to the tautomeric equilibrium in intramolecular hydrogen bond. Dependencies of the HOMA aromaticity index and electron density at the critical points defining aromaticity and electronic state of the chelate chain on the transition state (TS), OH and HN tautomeric forms have been obtained

Multi-Level Micromachined Systems-on-a-Chip: Technology and Applications

Researchers at Sandia have recently designed and built several research prototypes, which demonstrate that truly complex mechanical systems can now be realized in a surface micromachined technology. These MicroElectro- Mechanical Systems (MEMS) include advanced actuators, torque multiplying gear tmins, rack and pinion assemblies, positionable mirrors, and mechanical discriminators. All of tile mechanical components are batch fabricated on a single chip of silicon using the infrastructure origimdly developed to support today's highly reliabk; and robust microelectronics industry. Sand ia is also developing the technology 10 integrate microelectronic circuits onto the s,ime piece of silicon that is used to fabricate the MEMS devices. This significantly increases sensitivity and reliability, while fhrther reducing package size and fabrication costs. A review of the MEMS technology and capabilities available at Sandia National Laboratories is presented

Micromachined systems-on-a-chip: Infrastructure, technology and applications

A review is made of the infrastructure, technology and capabilities of Sandia National Laboratories for the development of micromechanical systems that have potential space applications. By incorporating advanced fabrication processes, such as chemical mechanical polishing, and several mechanical polysilicon levels, the range of micromechanical systems that can be fabricated in these technologies is virtually limitless. Representative applications include a micro-engine driven mirror, and a micromachined lock. Using a novel integrated MEMS/CMOS technology, a six degree-of-freedom accelerometer/gyroscope system has been designed by researchers at U.C. Berkeley and fabricated on the same silicon chip as the CMOS control circuits to produce an integrated micro-navigational unit

Clar's Theory, STM Images, and Geometry of Graphene Nanoribbons

We show that Clar's theory of the aromatic sextet is a simple and powerful tool to predict the stability, the \pi-electron distribution, the geometry, the electronic/magnetic structure of graphene nanoribbons with different hydrogen edge terminations. We use density functional theory to obtain the equilibrium atomic positions, simulated scanning tunneling microscopy (STM) images, edge energies, band gaps, and edge-induced strains of graphene ribbons that we analyze in terms of Clar formulas. Based on their Clar representation, we propose a classification scheme for graphene ribbons that groups configurations with similar bond length alternations, STM patterns, and Raman spectra. Our simulations show how STM images and Raman spectra can be used to identify the type of edge termination