VB calculations with orthogonal basis functions

As a first step in the development of a semiempirical VB method,ab initio VB calculations were performed to obtain potential energy curves for the molecules HF and BeH₂ and the energy profile of the collinear exchange reaction F + H₂ HF + H. The applicability of the method is discussed with particular emphasis on the calculation of integrals over OAO's, the choice of valence structures to be included in the CI scheme and the interpretation of the wave function in terms of OAO's.     

Unimolecular binary half-adders with orthogonal chemical inputs

Unimolecular half-adders based upon an arylvinyl-bipyridyl fluorophore platform were demonstrated where all the chemical input combinations were fully processed by half-adder molecules to generate the arithmetic results of the entire truth table.     

Three-dimensional electron cryomicroscopy of ribosomes

Single particle electron cryomicroscopy is nowadays routinely used to generate three-dimensional structural information of ribosomal complexes without the need of crystallization. A large number of structures of functional important ribosomal complexes have thus been determined using this technique. In E. coli 70S ribosomes all three tRNA binding sites could be localized. The ternary complex of EF-TutRNAGTP that delivers the tRNA to the ribosome was directly visualized in a ribosomal complex blocked by the antibiotic kirromycin. Three different functional states of translocation have been studied and the respective EF-G binding sites have been mapped. The level of resolution achievable with electron cryomicroscopy allows conformational changes in the domain structures of elongation factors to be modelled in terms of rigid body movements. Structural information on eukaryotic ribosomes is also available for yeast and mammalian 80S ribosomes. The structural differences between rabbit 80S and E. coli 70S ribosomes could be interpreted in terms of ribosomal RNA expansion segments in the 18S and 23S RNA. The EF-G homologue EF2 was mapped analysing the structure of an 80SEF2sodarin complex and most recently the binding of a hepatitis C virus IRES element to a yeast 40S subunit has been studied. The first electron cryomicroscopical 3D reconstructions have further been used to overcome the initial phasing problems in X-ray crystallographic studies of the ribosome facilitating structure determination of the recent atomic resolution structures of the 30S and 50S ribosomal subunits. In turn, the knowledge of the atomic structure of the ribosome makes detailed interpretations of cryo-EM maps possible at approximately 20 A resolution.     

Consolidating molecular AND logic with two chemical inputs

A novel molecular AND logic gate 1 is demonstrated based on the competition between fluorescence and photoinduced electron transfer (PET). It is constructed according to a 'receptor2-spacer-fluorophore-spacer-receptor1-spacer-fluorophore-spacer-receptor2' format where receptor1 is a tertiary amine, receptor2 is a benzo-15-crown-5 ether and the fluorophore is an anthracene moiety, which are separated from each other by methylene spacers. The fluorescence response in methanol is significantly enhanced only when both H+ and Na+ are the inputs at high enough concentrations in accordance with AND logic. Cs+ behaves similarly to Na+, but with a lower fluorescence enhancement, whereas the other alkali metal cations are not effective. Electrospray ionization mass spectrometry provides evidence for formation of 1:1 and 1:2 (1:metal) complexes with alkali cations, and formation of a 1:2:1 (1:metal:proton) complex in the additional presence of acid.     

A triethylenetetramine bearing anthracene and benzophenone as a fluorescent molecular logic gate with either-or switchable dual logic functions

Fluorescence behaviors of a triethylenetetramine bearing anthracene (AN) and benzophenone (BP) fragments at the respective ends, L1, have been studied in water, where effects of pH (H+) and metal cations on the emission properties have been studied in detail. L1 behaves as a fluorescent molecular logic gate driven by H+ (Input1) and metal cations (Input2) as input chemicals. The most notable feature of L1 is that this molecule expresses the "either-or" switchable dual logic functions. Operation of L1 with Cu2+ as Input2 expresses the INHIBIT logic function, where a strong AN fluorescence appears only at pH 4 (with H+) without Cu2+ [Input1(1)-Input2(0)]. In contrast, operations of L1 with all other metal cations as Input2 express the TRANSFER logic function, where the presence of H+ allows strong AN fluorescence regardless of whether the metal cation exists or not [Input1(1)-Input2(0); Input1(1)-Input2(1)]. These emission switching behaviors of L1 are driven by the difference in the coordination stability between L1 and metal cations and the photoinduced intramolecular electron and energy transfer processes: (i) a pH-induced electron transfer from unprotonated nitrogen atoms of the polyamine chain to the photoexcited AN [ELT(N-->AN*)]; (ii) a pH- and metal coordination-induced electron transfer from the photoexcited AN to the ground-state BP [ELT(AN*-->BP)]; and (iii) a Cu2+ coordination-induced energy transfer from the photoexcited AN to Cu2+ [ENT(AN*-->Cu2+)].     

Isolation of ribosomes from cotton seeds

Summary 1. It has been established that the method of precipitation with ethanol in the presence of an increased concentration of Mg²⁺ can be used for the rapid isolation of the ribosome fraction from plant material.2. The optimum conditions for the complete precipitation of the ribosome fraction from a homogenate of cotton seeds have been selected.3. By treating an extract of the seeds with 0.5 M KCl it was possible to reduce the amount of tRNA in a preparation of the total rRNA.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 852–856, November–December, 1977.     

Molecular-scale logic gates

Currently available approaches to molecular-scale logic gates are summarized and compared. These include: chemically-controlled fluorescent and transmittance-based switches concerned with small molecules, DNA oligonucleotides with fluorescence readout, oligonucleotide reactions with DNA-based catalysts, chemically-gated photochromics, reversibly denaturable proteins, molecular machines with optical and electronic signals, two-photon fluorophores and multichromophoric transient optical switches. The photochemical principles of electron and energy transfer are involved in several of these approaches. More complex molecular logic systems with reconfigurability and superposability provide contrasts with current semiconductor electronics. Integration of simple logic functions to produce more complex ones is also discussed in terms of recent developments.     

Microelectrochemical logic circuits

We report microelectrochemical devices that mimic some functions of solid-state circuit components such as diodes and transistors. The operation of this new family of devices is enabled by a network of microfluidic electrochemical cells that communicate with one-another via conductive solutions and, in some cases, bipolar electrodes. The output of the devices can be either electrochemical or optical. The approach reported here is a first step toward the development of large-scale integrated electrochemical systems having parallel processing capabilities.     

Cellular microarrays for use with capillary-driven microfluidics

We present a method for the facile arraying of cells on microstructured substrates which should be suitable for cellular assays in autonomous microfluidic capillary systems (CSs). The CSs, which were designed and microfabricated in Si, have various microfluidic functional elements including reaction chambers wherein cellular arrays are located. Two methods for arraying the cells were explored. In the first method, a hydrophobic alkanethiol was microcontact-printed on the bottom surface of a microfluidic reaction chamber. The subsequent adsorption of protein-repellent alkanethiols around the printed areas and the deposition from solution of fibronectin (FN) on the hydrophobic areas resulted in an adhesive pattern for the attachment of living human breast cancer cells. This method was limited by the formation of cellular clusters, which proved difficult to remove selectively. The second method employed a poly(dimethylsiloxane) elastomer having oval recessed microstructures. The selective coating of the inner walls of the ovals with FN and the blocking of the mesas around the ovals with bovine serum albumin (BSA) permitted single or multiple cells to be arrayed depending on the size of the ovals. The possibility of sealing CSs with cells arrayed on poly(dimethylsiloxane) may provide a versatile platform for high-throughput experimentation down to the single-cell level. Figure The deposition of one or a few living cells in fibronectin-coated poly(dimethylsiloxane) microstructures results in cellular arrays, which can be interfaced with capillary-driven microfluidics     

DNA logic gates

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.     

A fluorescent molecular logic gate with multiply-configurable dual outputs

A simple molecule, L, diethylenetriamine bearing anthracene fragments at both ends, behaves as a fluorescent molecular logic gate with "multiply-configurable dual outputs", capable of demonstrating five different logic functions operated by proton (H+) and transition metal cations (Mn+) as inputs.     

Deoxyribozyme-based logic gates

We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.     

Role of geometrical dimensions in electrophoresis applications with orthogonal fields

The role of geometrical dimensions in electrophoresis applications with axial and orthogonal (secondary) electric fields is investigated using a rectangular capillary channel. In particular, the role of the applied orthogonal electrical field in controlling key parameters involved in the effective diffusivity and effective (axial) velocity of the solute is identified. Such mathematically friendly relationships are obtained by applying the method of spatial averaging to the solute species continuity equation; this is accomplished after the role of the capillary geometrical dimensions on the applied electrical field equations has been studied. Moreover, explicit analytical expressions are derived for the effective parameters, i.e., diffusivity and convective velocity as functions of the applied (orthogonal) electric field. Previous attempts (see Sauer et al., 1995) have only led to equations for these parameters that require numerical solution and, therefore, limited the use of such results to practical applications. These may include, for example, the design of separation processes as well as environmental applications such as soil reclamation and wastewater treatment. An illustration of how a secondary electrical field can aid in reducing the optimal separation time is included.