The application of elastic auxiliary air bag imprinting technology to the development of linear gradient micro‐structure replication processes

This study proposed an innovative imprinting process technology using an elastic auxiliary air bag imprinting mechanism, combined with poly(dimethylsiloxane) (PDMS) soft mold and UV–LED array photocuring equipment, to evenly imprint and reproduce a micro‐lens mold into a gradient micro‐lens structure in order to achieve linear gradient in micro‐structures. The structure defined by the proposed process technology is more continuous and smoother than that of the current semi‐conductor gray scale photomasking process technology. The process is simpler, faster, and less expensive and is a more effective option for satisfying the formation requirements of different structural heights. This study used pressure‐sensitive film to test and discuss gradient imprint force distribution. The test results suggested that different spring constants led to tilt impressions, which caused the PDMS soft mold to contact with the substrate surface at different pressures. The color depth distribution of the pressure‐sensitive film testing results indicated that the spring constant and pressure distribution were somewhat correlated. Hence, the height of structural formation can be controlled by different spring constants. Finally, SEM and surface profiler measurements suggested that different spring constants can result in different tilt degrees of the imprinting platform of air bag imprinting applications for the imprinting and reproduction of smooth, continuous micro‐lens array structures of different heights. Copyright © 2012 John Wiley & Sons, Ltd.     

The signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences

We present a new algorithm that enumerates molecular structures matching a predefined extended valence sequence or signature. The algorithm can construct molecular structures composed of about 50 non-hydrogen atoms in CPU seconds time scale. The algorithm is run to produce all molecular structures matching the binding affinities (IC(50)) of some HIV-1 protease inhibitors. The algorithm is also used to compute the degeneracy, or the number of molecular structures, corresponding to a given signature. Signature degeneracy is systematically studied for varying signature heights on four molecular series, alkanes, alcohols, fullerene-type structures, and peptides. Signature degeneracy is compared with similar results obtained with popular topological indices (TIs). As a general rule, we find that signature degeneracy decreases as the signature height increases. We also find that alkanes, alcohols, and fullerene-type structures comprising n non-hydrogen atoms are uniquely characterized by signatures of height n/4, while peptides up to 4000 amino acids can be singled out with signatures of heights as small as 2 and 3.     

Nano- and microscopic surface wrinkles of linearly increasing heights prepared by periodic precipitation

Arrays of surface wrinkles of linearly increasing heights (from tens of nanometers to tens of micrometers) were prepared via a spontaneous reaction-diffusion process based on periodic precipitation. The slopes, dimensions, and positions of the precipitation bands could be controlled precisely by adjusting the concentrations of the participating chemicals as well as the material properties of patterned substrates. Additional control of periodic precipitation by localized UV irradiation allowed for the preparation of discontinuous and curvilinear structures. The nonbinary 3D surface topographies were replicated into poly(dimethylsiloxane), and the applications of replicas in microfluidics, microseparations, and cell biology have been suggested.     

Fragmentation and isomerization of 1,2-dimethylcyclobutane

The potential surface of 1,2-dimethylcyclobutane is investigated with respect to fragmentation and isomerization by the semiempirical MO method SINDO1. Energy and geometry of eight transition states and four intermediates are determined for the nonconcerted fragmentations under optimization of all internal coordinates. We find that symmetric cleavage ofcis-dimethylcyclobutane is the most favored process leading to fragmentation. Whereas the symmetric elimination involves two different barrier heights, the asymmetric elimination involves only two equal barrier heights. The possibility of isomerization ofcis- totrans- dimethylcyclobutane was also studied and revealed two different barrier heights lower than the corresponding heights for fragmentation.     

Global reaction route mapping on potential energy surfaces of formaldehyde, formic acid, and their metal-substituted analogues

Global reaction route mapping of equilibrium structures, transition structures, and their connections on potential energy surface (PES) has been done for MCHO (M = H, Li, Na, Al, Cu) and HCO2M (M = H, Li). A one-after-another technique based on the scaled hypersphere search method has been successfully applied to exploring unknown chemical structures, transition structures, and reaction pathways for organometallic systems. Upon metal substitution, considerable changes of stable structures, reaction pathways, and relative heights of transition structures have been discovered, though some features are similar among the analogues. Al and Cu atoms were found to behave as very strong scissors to cut the CO double bond in MCHO. Energy profiles of the CO insertion into Li-H and Li-CH3 bonds were found to be very similar, especially around the structures where the Li atom is not directly connected with the methyl group, which indicates little effects of alkyl substitution on the reaction route topology.     

Comparative theoretical study of transition structures,barrier heights,and reaction energies for the intramolecular tautomerization in acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems

The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2/6-31G**, MP2/6-311++G**, and MP2/6-311++G (3df,2p) levels. The geometry, electronic structure, harmonic vibrational frequencies, and transition vector associated with the transition structures as well as the relative stabilities of different isomers and barrier heights were analyzed. The dependence of these properties upon theoretical methods is analyzed and discussed. The transition structures are four-membered rings and the corresponding transition vectors are associated to collective fluctuations. The 1,3 intramolecular hydrogen migration is much more advanced than are the hybridization changes on donor and acceptor centers at the transition structure. The corresponding barrier heights can be related to the change of bond orders and acid/base properties of these centers. A comparison of the results obtained with different methods renders that the nature of the transition structure seems to be a rather robust entity. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 9–24, 1998     

Electrostatic Interactions That Determine the Rate of Pseudorotation Processes in Oxyphosphorane Intermediates: Implications with Respect to the Roles of Metal Ions in the Enzymatic Cleavage of RNA

The enzymatic cleavage of RNA takes place via a cyclic pentacoordinate oxyphosphorane intermediate/transition state. We carried out ab initio investigations on the neutral cyclic oxyphosphorane, which exists as a stable intermediate. As a consequence of the conformational preferences of the pentacoordinate trigonal bipyramidal intermediates, the rotation of the P-OH bonds is strongly coupled with the reaction coordinate for the pseudorotation process. In addition, the neutral PF(4)OH species has a higher barrier to pseudorotation than the corresponding anionic species PF(4)O(-). These findings are related to the positive charge of the hydrogen atoms on the equatorial oxygens in the trigonal bipyramidal structures: the hydrogen atoms preferably adopt eclipsed positions relative to the axial ligands. Fixing the cationic species in these regions causes an increase in the barrier heights for pseudorotation processes and, thus, prevents isomerization by pseudorotation. Consequently, metal coordination in the double-metal ion mechanism for enzymatic cleavage of RNA should serve to exclusively stabilize the trigonal bipyramidal intermediate/transition state for the in-line attack and departure process.     

Classification of monosubstituted phenyl rings by branching tree methods using infrared and raman peak heights

A branching tree scheme is proposed and evaluated for classifying monosubstituted benzenes by the structure of the part of a substituent which lies near the phenyl ring. A large group having the same atom attached to the phenyl ring is divided into subgroups having a more highly defined structure. Each subgroup is then further divided into still smaller subgroups having still more highly defined structures. Combined sets of infrared and Raman peak heights for bands characteristic of the phenyl ring vibrations are used as pattern vectors. A statistical linear discriminant method is used to correlate the peak heights of groups having similar near-the-ring structure. The stepwise and overall success rates are given for each level of classification.     

Spin labeling methods in molecular biology : G.I. Likhtenshtein,John Wiley & Sons,New York,London, Sydney and Toronto, 1976, pp. xiii + 258, price £26.00

As a consequence of intramolecular vibrations distorted apparent structures may result from an electron diffraction analysis of molecules possessing symmetrical equilibrium configuration. The amount of torsional distortion gives information concerning the barrier height to internal rotation. An approach is suggested to estimate barrier heights on the basis of average torsional angles as determined from electron diffraction, and expressions of the rotation-dependent distances as obtained from a Taylor expansion by neglecting higher order terms.     

Non-Planar Structures of Sterically Overcrowded Trialkylamines

Several amines with three bulky alkyl groups at the nitrogen atom, which exceed the steric crowding of triisopropylamine significantly, were synthesized, mainly by treating N-chlorodialkylamines with Grignard reagents. In six cases, namely tert-butyldiisopropylamine, 1-adamantyl-tert-butylisopropylamine, di-1-adamantylamines with an additional N-cyclohexyl or N-exo-2-norbonyl substituent, as well as 2,2,6,6-tetramethylpiperidine derivatives with N-cyclohexyl or N-neopentyl groups, appropriate single crystals were generated that enabled X-ray diffraction studies and analysis of the molecular structures. The four noncyclic amines adopt triskele-like conformations, and the sum of the three C−N−C angles is always in the range of 351.1° to 352.4°. Consequently, these amines proved to be structurally significantly flatter than trialkylamines without steric congestion, which is also signalized by the smaller heights of the NC₃ pyramids (0.241–0.259 Å). There is no clear correlation between the heights of these pyramids and the degree of the steric crowding in the new amines, presumably because steric repulsion is partly compensated by dispersion interaction. In the cases of the two heterocyclic amines, the steric stress is smaller, and the molecular structures include quite different conformations. Quantum chemical calculations led to precise gas-phase structures of the sterically overcrowded trialkylamines exhibiting heights of the NC₃ pyramids and preferred molecular conformers which are similar to those resulting from the X-ray studies.     

Theoretical study of isomerization and dissociation transition states of C3H5O radical isomers: ab initio characterization of the critical points and statistical transition-state theory modeling of the dynamics

I use coupled-cluster theory and a modest basis set, aug-cc-pVDZ, to calculate structures and harmonic vibrational frequencies of local minima and transition states on the C(3)H(5)O potential energy surface. Accurate energies are computed using explicitly correlated coupled-cluster methods and a large basis set, cc-pVQZ-F12, to approach the one-particle basis set limit. My computations characterize eight additional stable radical structures on the global potential energy surface for this system. Additionally, this study encompasses many more isomerization and dissociation pathways, both between previously known intermediates and ones first characterized here. Analysis of the transition states and statistical transition-state theory results shows that energetically small barriers connect many of the alkenol and epoxide intermediates to the straight-chain alkoxy isomers, leading to significant branching to these alkoxy radical intermediates. Facile isomerization to these alkoxy intermediates is significant because the barrier heights leading to H + acrolein and HCO + C(2)H(4) product channels are energetically accessible even at low vibrational energies. The low dissociation barrier heights and loose transition states of these pathways result in unimolecular dissociation as opposed to isomerization to a different C(3)H(5)O intermediate.     

Irreversible Collapse of Poly(vinyl stearate) Monolayers at the Air-Water Interface

The collapse of Langmuir monolayers of poly(vinyl stearate) (PVS) at the air-water interface has been investigated by combined measurements of the surface pressure-area isotherms and Brewster angle microscopy (BAM). Atomic force microscopy (AFM) has been used to gain out-of-plane structural information on collapsed films transferred onto a solid substrate by a modified version of the inverse Langmuir-Schaefer deposition method. At high areas per monomer repeat unit, BAM imaging revealed that the films are heterogeneous, with large solidlike domains (25-200 mum in diameter) coexisting with liquidlike domains. Upon film compression, the domains coalesced to form a homogeneous monolayer before the film collapsed at constant pressure, forming irreversible three-dimensional (3D) structures. BAM images showed that two 3D structures coexisted: buckles of varying width extending across the surface and perpendicular to the direction of the compression and dotted islandlike structures. Upon expansion, the film fractured and both 3D protrusions persisted, explaining the marked hysteresis recorded in the Langmuir isotherms. Experiments with AFM confirmed the 3D nature of both protrusions and revealed that many buckles contain substructures corresponding to narrow buckles whose heights are a multiple of a single bilayer. Additionally, many multilayer islands with diameters spanning from 0.2 mum to over 3.5 mum were characterized by varying heights between 2 nm and up to over 50 nm. The key to the formation of the irreversible 3D structures is the presence of large inhomogeneities in the PVS monolayer, and a generalized phenomenological model is proposed to explain the collapse observed.     

Conformational energies, rotational barrier heights and molecular structures in C(CH2X)4 molecules (X=F, Cl, Br)

The conformational energies, rotational barrier heights and molecular structures in C(CH₂X)₄ molecules (X=F, Cl, Br) based on molecular-mechanics calculations have been obtained. The results from these calculations are compared with the experimental gas-phase results.     

Water-induced reconstruction that affects mobile ions on the surface of calcite

Time-sequenced contact-force micrographs show that the (104) calcite cleavage surface reconstructs in humid air through pit formation and film growth. After 8 h at 80% relative humidity (RH), 50% to 80% of the surface is covered by islands that are flat-topped and 1-nm high. The lateral growth rates of individual islands are 4.2+/-0.4 nm min-1 in the 41 direction and 1.8+/-0.4 nm min-1 in the 48 direction, resulting in islands having distinct major and minor axes. On some samples, a contiguous, 1.5-nm-high film rapidly grows between the islands and the pits. The areal expansion rate of the film is 500 times faster than that of the islands. Gaps between the contiguous film and the islands expand and contract, which suggests that mass is exchanged between them and that both are loosely bound. Complementing the topographic images, polarization heights are simultaneously measured by polarization-force microscopy. The polarization heights of the islands and the contiguous film are -6 to -10 nm and -4 to -5 nm, respectively, compared to their respective topographic heights of +1.0 and +1.5 nm. Under our experimental conditions, the polarization heights are a surrogate for the local dielectric constant of the sample epsilon and arise from a convolution of the mobility and the density of surface ions. The polarization heights imply that epsilonsubstrate>epsilonfilm>epsilonisland. Changes in topographic and polarization heights at 20% and 50% RH suggest that the structures of the islands are in dynamic equilibrium with the adsorbed water. Our evidence suggests that the islands contain loosely bound water and may therefore be a hydrated calcium carbonate phase stabilized by the calcite surface.     

Organized collapse structures in mixtures of chiral ethyl 2-azido-4-fluoro-3-hydroxystearates

Monolayers of enantiomeric compounds as well as diastereomeric mixtures and racemic/diastereomeric mixtures of ethyl 2-azido-4-fluoro-3-hydroxystearates have been investigated using surface pressure-area isotherms and Brewster angle microscopy. All monolayers collapse out of the liquid-expanded phase, forming 3D collapse structures which were visualized with scanning force microscopy. The enantiomeric compound and the diastereomeric mixtures form unique fiber-like network structures with heights between 20 and 40 nm. Interestingly, the shape of the enantiomeric fiber structures is straight, whereas the diastereomeric mixtures exhibit curved fibers of different sizes. The racemic mixture however forms circular 10 nm high and 20-50 microm broad structures. The shape of unconventional collapse structures could be changed by using distinct ratios of diastereomeric or racemic/diastereomeric mixed compounds.     

Conformational structures, energies, rotational barrier heights and torsional force constants in halogenated methyl-silanes obtained by molecular-mechanics calculations

Conformational structures, energies, barrier heights and torsional force constants in halogenated (F, Cl, Br) methyl-silanes have been obtained by molecular-mechanics calculations. A comparison of the ethan-like molecules with central bonds C---C, Si---C and Si---Si has been made. It is predicted that, for halogenated methyl-silanes, the difference in conformational energy between anti and gauche conformers is small.     

Pillar-structured microchannels for on-chip liquid chromatography: evaluation of the permeability and separation performance

The chromatographic characteristics were determined for a set of microfabricated separation channels structured with cylindrical and diamond-shaped pillars with a characteristic size of 5 microm. Channels with different structures and porosities were etched in a silicon wafer using lithographic techniques. The permeability for flow of the channels was shown to increase strongly with the overall porosity. Diamond-shaped pillars appeared to yield a slightly higher permeability than cylindrical pillars at the same channel porosity. Compared to packed columns, permeabilities were higher by a factor of up to 5. Band dispersion in the channels was measured with an unretained fluorescent probe compound using a fluorescence microscope. A relatively large variation in the observed plate heights between channels was found, which was mainly attributed to the inaccurate geometry of the structure close to the side walls. Reduced plate heights between 0.2 and 1.0 were obtained. The lowest plate heights were found for channels with low porosity. The chromatographic impedances were calculated and compared to the values for the traditional chromatographic systems. For one of the structured microchannels the impedance was found to be more than ten times lower than for a column packed with nonporous spherical particles. With the data collected, predictions are given on the possibilities in terms of efficiency and speed offered by structured microchannels for pressure-driven separations, taking practical constraints into account.     

Structure Optimisation of Large Transition‐Metal Complexes with Extended Tight‐Binding Methods

Large transition‐metal complexes are used in numerous areas of chemistry. Computer‐aided theoretical investigations of such complexes are limited by the sheer size of real systems often consisting of hundreds to thousands of atoms. Accordingly, the development and thorough evaluation of fast semi‐empirical quantum chemistry methods that are universally applicable to a large part of the periodic table is indispensable. Herein, we report on the capability of the recently developed GFNn‐xTB method family for full quantum‐mechanical geometry optimisation of medium to very large transition‐metal complexes and organometallic supramolecular structures. The results for a specially compiled benchmark set of 145 diverse closed‐shell transition‐metal complex structures for all metals up to Hg are presented. Further the GFNn‐xTB methods are tested on three established benchmark sets regarding reaction energies and barrier heights of organometallic reactions.