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.     

Sliding on DNA: From Peptides to Small Molecules

Many DNA binding proteins utilize one‐dimensional (1D) diffusion along DNA to accelerate their DNA target recognition. Although 1D diffusion of proteins along DNA has been studied for decades, a quantitative understanding is only beginning to emerge and few chemical tools are available to apply 1D diffusion as a design principle. Recently, we discovered that peptides can bind and slide along DNA—even transporting cargo along DNA. Such molecules are known as molecular sleds. Here, to advance our understanding of structure–function relationships governing sequence nonspecific DNA interaction of natural molecular sleds and to explore the potential for controlling sliding activity, we test the DNA binding and sliding activities of chemically modified peptides and analogs, and show that synthetic small molecules can slide on DNA. We found new ways to control molecular sled activity, novel small‐molecule synthetic sleds, and molecular sled activity in N‐methylpyrrole/N‐methylimidazole polyamides that helps explain how these molecules locate rare target sites.     

Visual Displays that Directly Interface and Provide Read‐Outs of Molecular States via Molecular Graphics Processing Units

The monitoring of molecular systems usually requires sophisticated technologies to interpret nanoscale events into electronic‐decipherable signals. We demonstrate a new method for obtaining read‐outs of molecular states that uses graphics processing units made from molecular circuits. Because they are made from molecules, the units are able to directly interact with molecular systems. We developed deoxyribozyme‐based graphics processing units able to monitor nucleic acids and output alphanumerical read‐outs via a fluorescent display. Using this design we created a molecular 7‐segment display, a molecular calculator able to add and multiply small numbers, and a molecular automaton able to diagnose Ebola and Marburg virus sequences. These molecular graphics processing units provide insight for the construction of autonomous biosensing devices, and are essential components for the development of molecular computing platforms devoid of electronics.     

Anion Sensors as Logic Gates: A Close Encounter?

Computers have become smarter, smaller, and more efficient due to the downscaling of silicon‐based components. Top‐down miniaturisation of silicon‐based computer components is fast reaching its limitations because of physical constraints and economical non‐feasibility. Therefore, the possibility of a bottom‐up approach that uses molecules to build nano‐sized devices has been initiated. As a result, molecular logic gates based on chemical inputs and measurable optical outputs have captured significant attention very recently. In addition, it would be interesting if such molecular logic gates could be developed by making use of ion sensors, which can give significantly sensitive output information. This review provides a brief introduction to anion receptors, molecular logic gates, a comprehensive review on describing recent advances and progress on development of ion receptors for molecular logic gates, and a brief idea about the application of molecular logic gates.     

Force–Spectrum Relations for Molecular Optical Force Probes

Force probes allow real‐time monitoring of forces acting in different regions of large molecules and are potentially suited for the investigation of structural changes occurring in macromolecules during, e. g., folding processes. 1 – 10 Such information is crucial for the understanding of mechanochemical reactivity. 2 , 3 , 6 , 7 To this end, small molecular force probes can be incorporated into large molecules. 2 , 3 , 11 – 13 Some of the available systems are based on mechanochromism, the change of the UV/Vis absorption spectrum of a molecule under mechanical stress. 1 , 14 Herein we propose the idea of using molecular force probes in which the point‐group symmetry is reduced as a result of mechanical deformation. This effect leads to significant and characteristic changes in the UV/Vis, IR, and Raman spectra of the deformed molecules, which were determined using computational methods. Beneficially, these changes are reversible and occur even if the applied forces are small.     

Accurate lattice energies of organic molecular crystals from periodic turbomole calculations

Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom‐centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non‐covalently bound organic molecular crystals. The accuracy and convergence of results with basis set size and k‐space sampling from periodic calculations is evaluated for the two reference molecules benzoic acid and naphthalene. For the X23 benchmark set of small molecular crystals accurate lattice energies are obtained using the PBE‐D3 functional. In particular for hydrogen‐bonded systems, a sufficiently large basis set is required. The calculated lattice energy differences between enantiopure and racemic crystal forms for a prototype set of chiral molecules are in good agreement with experimental results and allow the rationalization and computer‐aided design of chiral separation processes. © 2018 Wiley Periodicals, Inc.     

Molecular Pom Poms from Self‐Assembling α,γ‐Cyclic Peptides

The hierarchical self‐assembly properties of a dimer‐forming cyclic peptide that bears a nicotinic acid moiety to form molecular pom‐pom‐like structures are described. This dimeric assembly self organizes into spherical structures that can encapsulate small organic molecules owing to its porosity and it can also facilitate metal deposition on its surface directed by the pyridine moiety.     

分子基逻辑材料*

在适当的条件下分子开关将输入的信息转换为输出信号,利用这一特点,可在分子体系根据二进位布尔逻辑规则实现信号转换。目前,用化学体系进行基本的布尔逻辑功能执行 (PASS、YES、NOT、AND、NAND、OR、NOR、XNOR和INH)都已成为可能。在此基础上,逻辑门的整合与编程,以及更进一步的复杂分子运算开始受到人们的关注。迄今为止,以高灵敏性的荧光输出信号为主,人们在分子水平上设计实现了多种复杂的逻辑电路,包括组合逻辑电路和时序逻辑电路等,并开始涉及信息处理的安全平台设计。本文主要介绍了近年来利用分子荧光开关体系模拟数字逻辑电路过程中所取得的最新进展,对分子逻辑电路研究的热点和问题进行了展望。     

Revisiting the Optimal Nano‐Morphology: Towards Amorphous Organic Photovoltaics

Organic photovoltaic cells commonly use an active layer with a polycrystalline bulk heterojunction. However, for simplifying the fabrication process, it may be worthwhile to use an amorphous active layer to lessen the burden on processing to achieve optimal performance. While polymers can adopt amorphous phases, molecular glasses, small molecules that can readily form glassy phases and do not crystallize over time, offer an appealing alternative, being monodisperse species. Our group has developed a series of reactive molecular glasses that can be covalently bonded to chromophores to form glass‐forming adducts, and this strategy has been used to synthesize glass‐forming donor and acceptor materials. Herein, the results of devices incorporating these materials in either partially or fully amorphous active layers are summarized. Additionally, these molecular glasses can be used as ternary components in crystalline systems to enhance efficiency without perturbing the morphology.     

DNA‐backbone radio resistivity induced by spin blockade effect

Coherent control of OH‐free radicals interacting with the spin‐triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet‐triplet resonance is developed. We illustrate that the spin‐triplet state in DNA molecules can be efficiently populated, as the spin‐injection rate can be tuned to be orders of magnitudes greater than the decay rate due to small spin‐orbit coupling in organic molecules. Owing to the nano‐second life‐time of OH free radicals, a non‐equilibrium free energy barrier induced by the injected spin triplet state that lasts approximately longer than one‐micro second in room temperature can efficiently block the initial Hydrogen abstraction and DNA damage. For a direct demonstration of the spin‐blockade effect, a molecular simulation based on an ab‐initio Car‐Parrinello molecular dynamics is deployed. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

A Pretreatment‐Free,Polymer‐Based Platform Prepared by Molecular Imprinting and Post‐Imprinting Modifications for Sensing Intact Exosomes

Exosomes are small (30–100 nm) membrane vesicles that serve as regulatory agents for intercellular communication in cancers. Currently, exosomes are detected by immuno‐based assays with appropriate pretreatments like ultracentrifugation and are time consuming (>12 h). We present a novel pretreatment‐free fluorescence‐based sensing platform for intact exosomes, wherein exchangeable antibodies and fluorescent reporter molecules were aligned inside exosome‐binding cavities. Such antibody‐containing fluorescent reporter‐grafted nanocavities were prepared on a substrate by well‐designed molecular imprinting and post‐imprinting modifications to introduce antibodies and fluorescent reporter molecules only inside the binding nanocavities, enabling sufficiently high sensitivity to detect intact exosomes without pretreatment. The effectiveness of the system was demonstrated by using it to discriminate between normal exosomes and those originating from prostate cancer and analyze exosomes in tear drops.     

In silico studies of 1,3(R):2,4(S)‐dibenzylidene‐D‐sorbitol as a gelator for polypropylene

The organic gelator 1,3(R):2,4(S)‐dibenzylidene‐D‐sorbitol (DBS) self‐organizes to form a 3‐D network at relatively low concentrations in a variety of nonpolar organic solvents and polymer melt. In this work, we have investigated the interactions between DBS molecules in polypropylene (PP) by molecular modeling. We have used quantum mechanics to elucidate the preferred geometry of one molecule and a dimer of DBS, and molecular mechanics and molecular dynamics to simulate pure DBS, pure PP, and mixture of DBS and PP as condensed phases, at various temperatures. It was found that inter‐ and intramolecular H‐bonds between DBS molecules are formed in PP in a much more pronounced manner than those formed in pure DBS. The most significant intermolecular H‐bonds are formed between the terminal hydroxyl groups. The most significant intramolecular H‐bonds are formed between O5 /H‐O6 groups. Due to the H‐bonds, DBS molecules form a rigid structure similar to liquid crystal forming molecules, which might explain their tendency to create nanofibrils. It seems that the aromatic rings do not contribute significantly to the intermolecular interactions. Their main role is probably to stiff the molecular structure. Temperature dependences of inter‐ and intramolecular interactions are different. Whereas intermolecular interactions peak heights decrease when temperature increases for pure DBS, the intramolecular interaction almost does not change. Copyright © 2012 John Wiley & Sons, Ltd.     

Logic Information Communication in a Fluorescent Molecular Switch

Based on the chemical‐sensitive fluorescence emission behaviors of the molecular switch 4‐bromo‐5‐methoxy‐2‐(2‐pyridyl)thiazole ( 2‐BMPT ), the communication of logic information between two functional units has been realized. With the rational control of the protonation and coordination reaction of 2‐BMPT , an upstream switching unit (a 1:2 demultiplexer) and two downstream data‐processing units are involved and interconnected in the communication. The two output states of the 1:2 demultiplexer serve as the initial input states of the two parallel downstream data‐processing units, which execute the information communication between the two circuit layers. Furthermore, in the parallel data‐processing layer, the logic gates of INHIBIT and YES accomplish their specific logic functions. Therefore, a molecular cascade circuit composed of an upstream switch and two downstream processing units has been constructed based on the chemical‐modulated fluorescence properties of 2‐BMPT .     

Natural molecular shells as open subsystems of small molecules

We compare the first few natural molecular shells of several small molecules to the corresponding “restricted Hartree‐Fock,” “second‐order Møller‐Plesset,” and “local density approximation” molecular shells. Occupation probabilities of each molecular shell are computed ab initio, especially the single‐occupation and double‐occupation probabilities, that is, the probabilities that the molecular shell is occupied by exactly one electron or by exactly two electrons. We observe that among corresponding molecular shells, the natural molecular shell has the least single‐occupation probability and the greatest double‐occupation probability. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Cascade configuration of logical gates processing information encoded in molecular potentials

We demonstrate that the outputs of two molecular devices encoding information as electrostatic potentials are able to trigger a third one and yield a correct truth table, thus demonstrating the possibility to successfully interconnect extremely low‐power consumption molecular devices. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Photo‐ and Redox‐Active Dendritic Molecules with Soft,Layered Nanostructures

Molecules with one photoactive group (porphyrin) and multiple redox‐active groups (ferrocenes) are described. The molecules are based on dendritic frameworks, with the ferrocenyl groups attached at the “internal” positions and the porphyrin attached at the focal point, leading to a characteristic layer architecture. Molecules of up to the third generation were synthesized and examined. The results of ¹H NMR spectroscopy and fluorescence quenching indicated that the ferrocenyl groups at the second layer approach the core porphyrin most closely, which is consistent with the results of molecular‐dynamics simulations. The electrochemistry of the molecules was also examined in detail, and a new formula is proposed for the analysis of multiple‐electron transfer in these “redox‐pool” molecules.     

Quantum chemical studies on the conformational behaviour of substituted banana‐shaped mesogens with a central 1,3‐phenylene unit

Ab initio and DFT calculations on the HF/STO‐3G and B3LYP/6‐31G(d) level were performed on the conformational behaviour of isolated banana‐shaped molecules of 1,3‐phenylene bis[4‐(4‐n‐hexyloxyphenyliminomethyl)benzoate] systems (P‐6‐O‐PIMB). The influence of small substituents in both the central phenyl ring and the external phenyl rings on the shape, polarity and flexibility of these molecules was investigated by one‐ and two‐fold relaxed potential energy scans in a systematic way. The effect of substituents on the global polarity of banana‐shaped mesogens was analysed by the magnitude and direction of the dipole moment and its components in relation to the long axis of the molecules. Moreover, a simple model for the calculation of the bending angle was tested for banana‐shaped molecules with a central 1,3‐phenylene unit. The findings for the isolated banana‐shaped molecules are correlated with solid state X‐ray and liquid crystalline state NMR results. Banana‐shaped molecules with both hexyloxy (P‐6‐O‐PIMB) and hexyl (P‐6‐PIMB) terminal chains are included to study the effect of substituents in the external phenyl rings on the flexibility of these chains. An attempt will be made to correlate the results with experimental findings on banana‐shaped mesogens.     

Orientation Control of Molecularly Functionalized Surfaces Applied to the Simultaneous Alignment and Sorting of Carbon Nanotubes

Self‐assembly has been relied upon for molecular alignment in many advanced technological applications. However, although effective, it is inherently limited in its capability for optimization. Despite the potential benefits, the seemingly fundamental strategy of external orientation control has yet to be realized. Herein we demonstrate an approach that allows control of the orientation of small molecules covalently bound to a surface. The method exploits an alignment relay technique, passing alignment information through a liquid‐crystal medium to small molecules to control surface functionalization events. The method is technically simple and can be carried out on a bench top without the need for specialized equipment. Moreover, we demonstrate the utility of the resulting surfaces to address two long‐standing problems in nanoscience: the sorting and alignment of single‐walled carbon nanotubes. This new method enabled significant alignment of the nanotubes as well as length and diameter sorting.     

Density Functional Theory Investigations on Vibrational Spectra,Molecular Structure,and Properties of the L‐Serine,L‐Cysteine,and L‐Aspartic Acid Molecules

In this paper, we present a thorough investigation of the conformational space to characterize all possible gas‐phase structures of the neutral L‐serine, L‐cysteine, and L‐aspartic acid molecules. A total of 120 trial structures were generated for L‐aspartic acid and 96 trial structures for L‐serine and L‐cysteine by combining all internal single‐bond rotamers. Various combinations of the Hartree–Fock and density functional theory/B3LYP methods with different bases were used to optimize all possible trial structures. The theoretical studies on the structure, harmonic vibrational spectra, and molecular properties of these amino acids are presented. The assignments of the calculated wave numbers resulting from potential energy distributions were performed using the VEDA 4 program to allow a good interpretation of the theoretical vibrational spectra of the title compounds. The fundamental harmonic frequencies were found to be in good agreement with data in the literature. A natural bond orbital analysis was performed to investigate the charge delocalization throughout the molecules for the three test compounds. Moreover, an extensive discussion of the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gap as well as other related molecular properties are reported.     

Synthesis of self‐healing supramolecular rubbers from fatty acid derivatives,diethylene triamine,and urea

We describe the synthesis of supramolecular self‐healing elastomers from vegetable oil fatty acid derivatives, diethylene triamine, and urea. Our strategy to obtain materials that are self‐healing but do not flow relies on the use of a wide molecular distribution of randomly branched oligomers equipped with self‐complementary and complementary hydrogen bonding groups. We prepared such oligomers with a two steps procedure. In the first step, diethylene triamine was condensed with dimer acids. In the second step, the oligomers obtained were allowed to react with urea. The molecules were characterized by NMR and IR spectroscopies and Monte‐Carlo simulations were used to analyze the molecular size distribution. The sensitivity to small variations of the experimental conditions has been examined and the robustness of the synthetic procedure optimized. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7925–7936, 2008