On the convergence of Z-averaged perturbation theory

Very high order open-shell Z-averaged perturbation theory (ZAPT) energies, equilibrium bond lengths, and harmonic vibrational frequencies have been computed for a suite of small molecules using a determinantal algorithm. The convergence of ZAPTn energies is compared to alternative Moller-Plesset (MP) perturbation theories built on restricted open-shell Hartree-Fock (ROMP, RMP, OPT1, and OPT2) and unrestricted Hartree-Fock (UMP) reference wave functions for NH(2) at three N-H bond lengths and for CN. The ZAPTn energy series closely parallel those of RMPn and ROMPn theories for these systems. Further, we examine the convergence of ZAPTn energies, equilibrium bond lengths (r(e)), and harmonic vibrational frequencies (omega(e)) for X (2)Sigma(g)(+) CN, X (4)Sigma(g) (-) C(2)(+), and b (2)Delta(g) C(2)(+), tracking oscillations in the energy series for the challenging latter system to order 1000. Finally, we obtain r(e) and omega(e) values from explicit ZAPT2 and ZAPT4 computations with a triple-zeta plus double polarization basis set. The ensuing results are very close to those from second- and fourth-order RMP and ROMP for the NO and CN molecules but are significantly closer to experiment in the case of (3)Sigma(g)(-) O(2). The ZAPTn series exhibit all the fascinating diversity of behavior previously observed for closed-shell MPn theory. Particularly encouraging is the ability of Feenberg transformations to remove erratic, strongly oscillatory, and divergent behavior that may occur in ZAPTn series and provide systematic improvements toward the full configuration interaction limit. In light of the appealing mathematical properties of ZAPT and similarity of results to those from the oft-applied RMP theory, coupled with the reductions in computational cost inherent in the ZAPT method relative to theories requiring different orbitals for different spins, we recommend low-order ZAPT for general applications to open-shell systems, particularly in cases where spin contamination is of concern.     

Stacking and Electrostatic Interactions Drive the Stereoselectivity of Silylium‐Ion Asymmetric Counteranion‐Directed Catalysis

Computational analysis shows that the enantioselectivity of asymmetric Lewis‐acid organocatalysis of the Diels–Alder cycloaddition of cyclopentadiene to cinnamates arises from stacking interactions that favor the addition of the diene to the more hindered face of the dienophile, while electrostatic interactions control the diastereoselectivity by selectively stabilizing the endo transition state. These results not only explain the stereoselectivity of these silylium‐ion‐ACDC reactions but should also guide the development of more effective ion‐pairing asymmetric organocatalysts.     

Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron–Sulfur Cluster through 15N Vibrational Frequency Shifts

The Rieske [2Fe–2S] cluster is a vital component of many oxidoreductases, including mitochondrial cytochrome bc1; its chloroplast equivalent, cytochrome b6f; one class of dioxygenases; and arsenite oxidase. The Rieske cluster acts as an electron shuttle and its reduction is believed to couple with protonation of one of the cluster′s His ligands. In cytochromes bc1 and b6f, for example, the Rieske cluster acts as the first electron acceptor in a modified Q cycle. The protonation states of the cluster′s His ligands determine its ability to accept a proton and possibly an electron through a hydrogen bond to the electron carrier, ubiquinol. Experimental determination of the protonation states of a Rieske cluster′s two His ligands by NMR spectroscopy is difficult, due to the close proximity of the two paramagnetic iron atoms of the cluster. Therefore, this work reports density functional calculations and proposes that difference vibrational spectroscopy with ¹⁵N isotopic substitution may be used to assign the protonation states of the His ligands of the oxidized Rieske [2Fe–2S] complex.     

Maze exploration and learning in C. elegans

The soil dwelling nematode, Caenorhabditis (C.) elegans, is a popular model system for studying behavioral plasticity. Noticeably absent from the C. elegans literature, however, are studies evaluating worm behavior in mazes. Here, we report the use of microfluidic mazes to investigate exploration and learning behaviors in wild-type C. elegans, as well as in the dopamine-poor mutant, cat-2. The key research findings include: (1)C. elegans worms are motivated to explore complex spatial environments with or without the presence of food/reward, (2) wild-type worms exhibit a greater tendency to explore relative to mutant worms, (3) both wild-type and mutant worms can learn to make unconditioned responses to food/reward, and (4) wild-type worms are significantly more likely to learn to make conditioned responses linking reward to location than mutant worms. These results introduce microfluidic mazes as a valuable new tool for biological behavioral analysis.     

Flow of microgel capsules through topographically patterned microchannels

We investigated the flow dynamics of microgel capsules in topographically patterned microfluidic devices. For microgels flowing through channel constrictions, or orifices, we observed three phenomena: (i) the effect of confinement, (ii) the role of interactions between the microgels and the channel surface, and (iii) the effect of the velocities of microgels prior to their passage through an orifice. We studied negatively charged alginate microgels and positively charged alginate microgels coated with N-(2-hydroxy)propyl-3-trimethylammonium chitosan chloride (HTCC). Aqueous dispersions of microgels were driven through poly(dimethyl siloxane) microchannels carrying a weak negative surface charge. The velocity of the continuous phase, and hence, the velocity of the microgels increased as they passed through topographically patterned orifices. Alginate microgels were observed to have a larger increase in velocity relative to HTCC-coated alginate microgels. This effect, which was attributed to electrostatic attraction or repulsion, was found to be strongest for orifices with dimensions close to the microgel diameter. For example, when 75 microm-diameter microgels flowed through a 76 microm orifice, alginate gels (negatively charged) experienced a 2x greater increase in velocity than HTCC-coated (positively charged) microgels. This effect was exaggerated at lower initial flow rates. For example, when 75 microm-diameter microgels flowed through an 80 microm orifice, a two-fold difference in the velocity changes of the two microgel types was observed when the initial flow rate was 275 microm s(-1), while a three-fold difference in velocity changes was observed when the initial flow rate was 130 microm s(-1). We speculate that these studies will be useful for modeling the flow of suspensions of cells or other biologically relevant particles for a wide range of applications.     

UHV STM I(V) and XPS studies of aryl diazonium molecules assembled on Si(111)

Molecular layers formed from 4-trifluoromethylbenzenediazonium tetrafluoroborate and 4-Methylbenzenediazonium tetrafluoroborate have been assembled on H-passivated Si(111) and studied by UHV STM and XPS. STM imaging shows well-developed Si(111) step edges and terraces both on Si(111):H and Si(111) substrates covered with a molecular layer. STM I(V) data acquired at different tip-substrate separations reveals a factor of approximately 10 enhancement in current for positive bias voltage when current flows through the 4-trifluoromethyl molecule when compared to the 4-methyl variant. The observed current enhancement in I(V) can be understood by comparing the projected density of states of the two molecule-Si systems calculated using a density functional theory local density approximation after geometry optimization was performed via the conjugate gradient method. XPS data independently confirm that H-passivated Si(111) remains oxygen free for short exposures to ambient conditions and provide evidence that the molecules chemically react with the silicon surface.     

Polyamides incorporating phosphine oxide groups. II. Aromatic polymers containing sulfone functionality

Four novel polyamides have been prepared in high yields by the polycondensation reactions of bis(3-carboxyphenyl)- and bis(4-carboxyphenyl)phenylphosphine oxide with 3,3′- and 4,4′-diaminodiphenylsulfone. The thermal properties of these materials were studied using differential scanning calorimetry and thermogravimetric analysis. It was found that the presence of both phosphine oxide and sulfonyl groups within the polymer backbone brought about remarkable modifications in the thermal behavior. Glass transition temperatures 40–50°C lower than those of conventional polyamides i.e., in the range 170–200°C, were recorded. However, we observed greater thermooxidative stability (5% weight loss at >410°C) and high char yield upon prolonged heating at 800°C (20–34%). Also, good solubility in polar aprotic solvents was observed for all polyamides together with some solubility in aqueous solvent mixtures, e.g. tetrahydrofuran/water (95:5). © 1997 John Wiley & Sons, Inc.     

Vibrational projection analysis: New tool for quantitatively comparing vibrational normal modes of similar molecules

A new method for quantitatively comparing calculated vibrational modes is described that relies on projecting the vectors describing the normal modes of one molecule onto those of a basis molecule. The procedure virtually automates the assignment of vibrational modes from one molecule to a second, structurally similar one. We illustrate the concept by using the classical Wilson modes of benzene as a basis for describing normal modes of the monosubstituted benzene derivatives phenol, phenol-d5, and phenol radical cation. These examples demonstrate the method's power for accurately assigning and comparing the normal modes of molecules perturbed by chemical substitution, isotopic substitution, or oxidation state. The vibrational projection analysis method—a special case of vector projection analysis—is compared and contrasted with total energy distribution analysis, perhaps the most commonly used technique for quantitatively comparing vibrational modes, and is found superior in each case when comparing normal modes. Vibrational projection analysis need not be limited to single molecules and quantum calculations, because normal modes may be obtained for much larger systems using molecular mechanics or molecular dynamics techniques. The method should therefore prove useful for interpreting the normal modes of ordered periodic solids and structures perturbed by noncovalent contacts, including proteins and polymers. The method may also prove useful in evaluating new computational methods by allowing direct, quantitative comparison of the vibrational modes obtained from different techniques. The power of this technique will make vibrational projection analysis a valuable tool for computational chemists as well as those using calculations to complement vibrational spectroscopic measurements. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1663–1674, 1998