Molecular logic: a half-subtractor based on tetraphenylporphyrin

Spectroscopic changes from a solution of the amphophile 5,10,15,20-tetraphenylporphyrin in N,N-dimethylformamide using inputs of acid (HClaq) and base (KOBut) are interpreted as XOR and INHIBIT logic operations. The combination of these two operations gives rise to a device that acts as a molecular half-subtractor.     

Deoxyribozyme-based half-adder

We have constructed a solution-phase array of three deoxyribozyme-based logic gates that behaves as a half-adder. Two deoxyribozymes mimic i(1)ANDNOTi(2) and i(2)ANDNOTi(1) gates that cleave a fluorogenic substrate, reporting through an increase in fluorescence emission at 570 nm. The third deoxyribozyme mimics an i(1)ANDi(2) gate and cleaves the other fluorogenic substrate, reporting through an increase in fluorescence emission at 520 nm. Together, this system represents the first example of a decision-making enzymatic network with two inputs and two outputs. Similar systems could be applied to control autonomous therapeutic and diagnostic devices.     

All-photonic molecular half-adder

One molecule acts as both an AND and an XOR Boolean logic gate that share the same two photonic inputs. The molecule comprises a half-adder, adding two binary digits with only light as inputs and outputs, and consists of three covalently linked photochromic moieties, a spiropyran and two quinoline-derived dihydroindolizines. The AND function is based on the absorption properties of the molecule, whereas the XOR function is based on an off-on-off response of the fluorescence to the inputs that results from interchromophore excited-state quenching interactions. The half-adder is simple to operate and can be cycled many times.     

Molecule-based photonically switched half-adder

A molecule-based binary half-adder with optical inputs and outputs has been demonstrated. The half-adder consists of two photochromic organic molecules in solution and a third-harmonic-generating crystal. One substance acts as an AND Boolean logic gate and the other as an XOR gate. Inputs are laser pulses at 1064 or 532 nm that initiate photoisomerization reactions. Outputs are the optical absorbance of a fullerene radical anion (AND gate) and fluorescence of a porphyrin (XOR gate). The system carries out binary addition based on the laser input pulses. Half-adders in combination are capable of carrying out all mathematical operations necessary for digital computing.     

A new redox-resettable molecule-based half-adder with tetrathiafulvalene

A new redox molecule-based half-adder with tetrathiafulvalene (TTF) was reported for the first time. This half-adder employs electrochemical and chemical oxidations (NOPF6) as input signals and absorbances at 350 and 435 nm as output signals. It is interesting to note that this new molecule-based half-adder shows reset capability by making use of the unique redox behaviors of TTF.     

Molecular beacon-based fluorescence biosensor for the detection of gene fragment and PCR amplification products related to chronic myelogenous leukemia

A novel fluorescence method has been established for the determination of gene fragment and PCR amplification products related to chronic myelogenous leukemia (CML). A molecular beacon (MB) which comprises a DNA loop section, a pair of fluorophore (tetramethoxyl rhodamine, TAMRA), and a quencher (4-(2-methyl-on-amino-azobenzene) benzoate, DABCYL) was designed. The loop sequence of MB was designed according to the DNA sequence relating to CML (type b3a2) which contained a single-stranded oligonucleotide. Before hybridization, the fluorescence from the TAMRA had been quenched by the DABCYL. After hybridization with the complementary DNA, the quencher will become far away from the TAMRA, and the fluorescence intensity detected will increase. Changes in the fluorescence intensity have a linear relationship with the concentration of complementary DNA (C) in the range of 4.0 × 10⁻⁹–3.2 × 10⁻⁸ mol/L, with a correlation coefficient of 0.9973; the detection limit was 6.0 × 10⁻¹⁰ mol/L (S/N = 3). The developed method has high selectivity, which can be used to discriminate single-base mismatch sequence. The method has been applied to detect the short-stranded CML DNA fragment (278 bp) with high sensitivity. This approach is a promising method for the detection of CML in real samples for medical diagnostics.     

2,2'-Bipyridyl]-3,3'-diol as a molecular half-subtractor

[structure/diagram: see text] Spectral responses at two different wavelengths revealed that BP(OH)2 ([2,2'-bipyridyl]-3,3'-diol) can function as a combinatorial logic circuit for a molecular half-subtractor with acid and base as input variables.     

A molecular half-subtractor based on a fluorescence and absorption dual-modal sensor for copper ions

A l-phenyl alanine derivative (L) could be used as a fluorescence and absorption dual-modal sensor, which was highly sensitive and selective to copper ion at physiological pH. We have drawn attention to the use of its copper complex to acquire a half-subtractor with parallel operating INHIBIT and XOR logic gates, by monitoring, fluorescence and absorbance as output signals, respectively.     

Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination

Molecular beacons (MBs) are oligonucleotide probes having a compact hairpin structure, with a fluorophore attached to one end and a quencher molecule attached to the other end. In its native state, the fluorophore is quenched by virtue of its proximity to the quencher molecule. Upon hybridization with its complementary oligonucleotide target, fluorescence is elicited due to a conformational change that results in separation of the fluorophore and quencher molecule. The present study describes the hybridization interaction of an MB to various complementary target sequences. The effects of temperature and length of complementary target sequences on hybridization were investigated using capillary electrophoresis and solution-based fluorescence techniques. Hybridization efficiency was dependent on the ability of the target sequences to destabilize the stem region by binding directly to the stem region. Optimal hybridization occurred between 40 and 50 degrees C for all targets tested, with the true target forming a more stable hybrid complex.     

Effective PET and ICT switching of boradiazaindacene emission: a unimolecular, emission-mode, molecular half-subtractor with reconfigurable logic gates

[reaction, structure: see text] We report a unimolecular system functioning as a combinatorial logic circuit for half-subtractor. The emission characteristics can be modulated by chemical inputs, and when followed at two different wavelengths, two functionally integrated logic gates XOR and INHIBIT are obtained. Both logic gates function in the emission mode, and with very large differences in the signal intensity allowing unequivocal assignment of logic-0 and logic-1.     

Detection of prolactin inducible protein mRNA, a biomarker for breast cancer metastasis, using a molecular beacon-based assay

Mortality due to breast cancer is increasingly linked to early, undetected metastasis, making methods for earlier detection acutely necessary. We describe the development of an assay based on molecular beacon (MB) chemistry with fluorescence detection to monitor a breast cancer biomarker for the analysis of breast cancer metastasis. The MB assay is based on the complementary base-pairing interactions of the MB nucleic acid with mRNA indicative of breast cancer metastasis. The presence of mRNA is characterized by an increase in the fluorescence intensity of the molecular beacon. The assay gives a linear, reproducible response to prolactin inducible protein mRNA, with a limit of detection in the high picomolar range. This method sensitively and specifically identifies a biomarker directly in serum samples in minimal time and with a straightforward procedure, dramatically reducing the total time for sample analysis over current methods from days to hours. The potential impact of this work in detection and understanding of breast cancer metastasis lies in improvements in simplicity, accuracy, and speed over current methods, which could allow for improved patient treatment and prognoses. Ultimately, additional sample throughput will result in better understanding of disease progression.     

Molecular Lamps and Molecular Golf Balls

The concave shielding of the active site of enzymes has been transferred to standard reagents of organic chemistry and concave reagents have been synthesized which possess a lamp-like geometry (concave 1,10-phenanthrolines 1–2, concave pyridines 3). The special concave geometry of these reagents is responsible for their selectivity in metal ion catalyzed (Pd-catalyzed allylations, Cu(I)-catalyzed cyclopropanations) and base catalyzed (acylation of alcohols by ketenes) reactions. For an easier recovery, these reagents have been attached to Merrifield polymers and to dendrimers. Higher generations of dendrimers loaded with concave reagents will possess a golf ball geometry.     

分子纳米技术与金属有机分子纳米体系

基于超分子自组装的分子纳米技术是一种新兴的高新技术。本文从金属矢量操纵的自组装分子纳米体系、自组装的纳米微反应器与超分子催化和自组装金属超分子高分子纳米材料等三个方面评述了分子纳米技术及其在构筑金属有机分子纳米体系中的发展现状 ,进一步阐述了“金属矢量”的概念 ,并首次提出建立“自组装子工具箱” ,探讨了分子纳米技术的发展方向。     

从分子构造到分子构型和分子构象（上）

分子构造(constitution)是指分子中原子相互联结的方式和次序,过去长期以来称为分子结构((structure),根据国际纯粹和应用化学联合会的建议,改为“构造”。“结构”一词应用在广泛的范围,例如物质结构、原子的电子结构等等。     

从分子构造到分子构型和分子构象（中）

我们从(上)文看到,化学家们最初认为物质的性质只决定于物质的分子组成,后来逐渐认识到物质的性质除决定于物质的分子组成外,还决定于分子构造.     

E-R分子轨道定域化方法与分子结合能

自编了E-R^[1]定域化计算程序,对HF、LiH、BH、Li₂、Be₂、CO和CH₄等分子作了计算。确定的酉变换算出的定域分子轨道正确。计算了各分子的定域分子轨道能量ε、加和能E′和结合能E″^[2],得到三点结论。     

两性聚电解质溶液的分子热力学模型和分子动力学模拟

从带电硬球混合物出发采用化学缔合理论建立了聚电解质和两性聚电解质溶液的分子热力学模型.用考虑溶剂的粘滞力和热浴随机力作用的分子动力学(MD)方法模拟了聚电解质和两性聚电解质溶液的渗透系数.对模型预测结果和MD模拟结果进行了比较,表明基于化学缔合理论的分子热力学模型可以用于聚电解质溶液和两性聚电解质溶液热力学性质的预测,对于均聚电解质溶液效果令人满意,对由直径不同的离子构成的聚电解质溶液,模型的预测效果变差,有待进一步改进.该模型对两性聚电解质溶液渗透系数的预测效果比对聚电解质溶液的预测效果更好.     

PuO3和PuO+3的分子结构与分子光谱

用相对论有效原子实势RECP和密度泛函(B3LYP, BHANDHLYP)、HF方法对PuO3的分子结构与分子光谱进行了研究.计算比较了C2v, D3h, C3v等构型以及计算方法等对PuO3分子能量和平衡结构的影响,结果表明中性的PuO3能够稳定存在,基态结构为C2v,状态为7B1 (B3LYP R1＝0.19143 nm, R2(＝R3)＝0.22057 nm, ∠OPuO＝102.2108°),比较而言PuO3分子还可能存在D3h结构的亚稳态7A2″,不存在稳定的C3v结构的PuO3分子.计算还同时首次给出了不同多重性的PuO3分子及其一价正离子PuO+3完整的能量、平衡几何结构、光谱数据、电荷布居、自旋密度、极化率与电偶极矩等系列数据.     

Molecular shape and flexoelectricity

Monte Carlo simulations were performed of systems of wedge-shaped objects formed from Gay-Berne ellipsoids joined to Lennard-Jones spheres. We studied two different wedge shapes, one more asymmetric than the other. The bend and splay flexoelectric coefficients were measured in the isotropic and smectic phases using linear response theory, and found to be negligibly small in the isotropic phase. We found a close connection between the properties of the intermolecular potential and the flexoelectric coefficients measured in the smectic phase. In particular, negligible bend coefficients were found for both shapes and a larger magnitude of the splay coefficient for the more prominent wedge, in accord with Meyer's original mechanism for flexoelectricity. The less prominent wedge produced a splay flexoelectric coefficient with the opposite sign due to the attractive tail of the intermolecular potential and the relative narrowness of the molecular head.