Influence of binding groups on molecular junction formation

We study the formation mechanism of molecular junctions using break-junction experiments. We explore the contribution of gold-atom rearrangements in the electrodes by analyzing the junction stretching length, the length of individual plateaus, and the length of the gold one-atom contacts. Comparing the results for alkane dithiols and diamines, we conclude that thiols affect gold electrode dynamics significantly more than amines. This is a vital factor to be considered when comparing different binding groups.     

Highly enantioselective Michael addition of nitroalkanes to chalcones using chiral squaramides as hydrogen bonding organocatalysts

A series of squaramide-based organocatalysts were facilely synthesized and applied as hydrogen bonding organocatalysts in the enantioselective Michael addition of nitroalkanes to chalcones. These organocatalysts promoted the Michael addition with low catalyst loading under high temperature (80 °C), affording the desired R or S enantiomers of the products flexibly in high yields with excellent enantioselectivities (93-96% ee) by the appropriate choice of organocatalysts.     

A molecular dynamics study of chloride binding by the cryptand SC24

The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol⁻¹. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural flexibility of the cryptand, leads to a decrease in the energy barrier, whereas, its structural rigidity is partially responsible for its selectivity.     

Covalent binding of biorecognition groups to solids using poly(hydromethylsiloxane) as linkage

By activating SiH bonds, poly(hydromethylsiloxane) can be covalently bound in a first step to various metal or polymer surfaces. In a second step, unreacted SiH bonds can be brought to react with organic compounds having adequate functional groups such as double or triple bonds, carbonyl or hydroxyl groups. This scheme is used to bind biorecognition groups to solids. The novel concept is demonstrated by attaching a newly synthesized biotin derivative to Au. It is shown that the immobilized biotin is capable of binding streptavidin.     

Substrate binding and activation via pendant hydrogen-bonding groups as an approach to biomimetic homogeneous catalysis

In a biomimetic approach to organometallic catalysis, pendant hydrogen-bonding groups are shown to influence the chemistry of ligand binding and activation in an iridium complex. Such groups can bind a substrate by hydrogen bonding and so offer the possibility of a biomimetic approach to catalysis where binding is controlled via molecular recognition. Because catalyst design in this area may be challenging, combinatorial and rapid screening methods may be needed to assay potential catalysts and initial progress on developing these methods for hydrosilation of alkenes and imines is described. Catalysis of aldehyde imination and the origin of pK_a changes of bound H₂ are discussed.     

Protons as the triggers to regulate hydrogen-bonding receptors

[reaction: see text] The protonation of alkylamines in two novel receptors results in intramolecular host-guest associations between the resulting ammonium ions and crown ether macrocycles. These interactions result in conformational changes of the receptors and prevent them from acting as hydrogen bond complements for uracil and carboxylate guest species.     

Effective potentials for spectator groups in molecular systems I. Potential curves and binding energies

Summary A method for representing inactive groups, i.e. spectator groups, in a molecular system by an effective potential is presented. The matrix elements for the spectator's short-range Hartree-Fock potential is stored in an intermediate AO basis, from which it can be transferred into the user basis for the active part of the molecular system. The longer-range of the potential is transferred via a (distributed) multipole expansion. The method is illustrated for the NH₃·X (X=NH₃, H₂O, HF) complexes: binding energies could be reproduced to within 5% by employing the effective NH₃ potential (whereby the lone pair was included in the active system), the entire NH₃·HF potential curve with a depth of 50 kJ/mol is reproduced within 2 kJ/mol if various intermediate basis sets are chosen. Technical details are discussed; the effective potential can directly be introduced in CI calculations.     

Duocarmycins binding to DNA investigated by molecular simulation

Duocarmycins are a potent class of antitumor agents, whose activity arises through their covalent binding to adenine nucleobases of DNA.(1-3) Here, we perform molecular dynamics (MD) and hybrid Car-Parinello QM/MM simulations to investigate aspects of duocarmycin binding to the d(pGpApCpTpApApTpTpGpApC) oligonucleotide. We focus on the derivatives (+)-duocarmycin SA (DSA) and (+)-duocarmycin SI (DSI), for which structural information of the covalent complex with the oligonucleotide is available, as well as on the related, but less reactive, NBOC-duocarmycin SA (NBOC-DSA), interacting with the same oligonucleotide. Comparison is made with adenine alkylation reaction in water performed by the smallest of these compounds (NBOC-DSA). The MD calculations suggest that, in noncovalent complexes, (i) drug binding causes a partial dehydration of the minor groove, without inducing a significant conformational changes, and (ii) DSA and DSI occupy a more favorable position for nucleophilic attack than NBOC-DSA, consistently with the lower reactivity of the latter. The QM/MM calculations, which are used to investigate the first step of the alkylation reaction, turn out to provide strongly underestimated free energy barriers. Within these approximations, our calculations suggest that an important ingredient for the experimentally observed DNA catalytic power is the polarization of the drug by the biomolecular scaffold.     

Modeling competitive guest binding to beta-cyclodextrin molecular printboards

Anchoring of functionalized guest molecules to self-assembled monolayers (SAMs) is key to the development of molecular printboards for nanopatterning. One very promising system involves guest binding to immobilized beta-cyclodextrin (beta-CD) hosts, with guest:host recognition facilitated by a hydrophobic interaction between uncharged anchor groups on the guest molecule and beta-CD hosts self-assembled at gold surfaces. We use molecular dynamics free energy (MDFE) simulations to describe the specificity of guest:beta-CD association. We find good agreement with experimental thermodynamic measurements for binding enthalpy differences between three commonly used phenyl guests: benzene, toluene, and t-butylbenzene. van der Waals interaction with the inside of the host cavity accounts for almost all of the net stabilization of the larger phenyl guests in beta-CD. Partial and full methylation of the secondary rim of beta-CD decreases host rigidity and significantly impairs binding of both phenyl and larger adamantane guest molecules. The beta-CD cavity is also very intolerant of guest charging, penalizing the oxidized state of ferrocene by at least 7 kcal/mol. beta-CD hence expresses moderate specificity toward uncharged organic guest molecules by van der Waals recognition, with a much higher specificity calculated for electrostatic recognition of organometallic guests.     

Synthesis of phosphorus-containing polyoxamacrocycles with one to two reactive thiophosphoryl chloride groups

Novel phosphorus-containing polyoxamacrocycles with one to two reactive thiophosphoryl chloride groups 5,6,7,8 were synthesized from bishydroxyl compounds 1,2,3,4 and thiophosphoryl chloride respectively.Their structures were confirmed by ~1H NMR,~(13)C NMR,~(31)p NMR and elemental analysis.     

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Synthesis of phosphorus-containing polyoxamacrocycles with one to two reactive thiophosphoryl chloride groups

Novel phosphorus-containing polyoxamacrocycles with one to two reactive thiophosphoryl chloride groups 5, 6, 7, 8 were synthesized from bishydroxyl compounds 1, 2, 3, 4 and thiophosphoryl chloride respectively. Their structures were confirmed by ^ 1H NMR, ^13C NMR, ^31p NMR and elemental analysis.     

A C3-symmetric colorimetric anion sensor bearing hydrazone groups as binding sites

Tris-hydrazone (1) functioned as a colorimetric chemosensor for a variety of anions such as F(-), AcO(-) and H(2)PO(4)(-). The anion binding could be easily detected by naked-eye according to color changes. The high binding ability of the receptor 1 to anions was further investigated by UV-vis absorption spectroscopy in DMSO. The results of job plot of the receptor 1 with different anions demonstrated that the stoichiometry of the complex between 1 and F(-) was 1:1 (1:anion) and the stoichiometry of the other complexes studied was 1:3 (1:anion).     

Use of ferrocene scaffolds as pendant groups in hairpin-type pyrrole-imidazole polyamide molecules showing sequence-selective binding to DNA duplexes

[reaction: see text] The synthesis and properties of new conjugate molecules, Fc-PIA, composed of ferrocene (Fc) and pyrrole-imidazole polyamides (PIA) are reported. As a PIA sequence, we chose Im-Py-Im/Py-Im-Py considering its future application to the SNPs detection of genes having a GCG/CGC sequence. Two types of Fc-containing linkers, i.e., ferrocene-1,1'-dicarboxamide and ferrocenecarboxamide, were designed, and several Fc-PIPA molecules having these linkers were synthesized. Titration studies by use of circular dichroism revealed that the carboxamide-type Fc-PIA could bind to the target DNA with an association constant of 10(7) M(-1). In contrast, ferrocene dicarboxamide-type compounds have slightly weaker affinity for the target DNA. However, the affinity could be recovered by replacing one of the pyrrole residues with beta-alanine. We carried out the CV measurement and observed quasi-irreversible oxidation of the ferrocene moieties in the Fc-PIA compounds. These properties of Fc-PIA indicate the potential usefulness of these molecules in electrochemical detection of genes.     

可再生型高价碘试剂亚碘酰二内酯在高效醇氧化中的应用研究

利用商品化的高价碘试剂亚碘酰二内酯(Iodosodilactone)作为最终氧化剂, 配合催化量的氮氧自由基2,2,6,6-四甲基哌啶-1-氧自由基(TEMPO)和当量的4-二甲氨基吡啶(DMAP)所组成的反应体系可以将含有不同官能团的伯醇快速高效地氧化为相应的醛且不会发生过度氧化; 将反应体系中的催化剂换为空间位阻较小的氮氧自由基1-甲基-2-金刚烷氮氧自由基(1-Me-AZADO)则可以将仲醇高效地氧化为相应的酮. 值得指出的是, 反应结束后Iodosodilactone的还原态2-碘-间苯二甲酸和DMAP可以通过简单的过滤及酸碱中和处理进行回收, Iodosodilactone的再生可通过用次氯酸钠/盐酸体系氧化2-碘-间苯二甲酸来高效实现.     

Rapid NMR screening of chloride receptors: uncovering catechol as a useful anion binding motif

This paper reports the application of a high-throughput 1H NMR screening method to the evaluation of potential anion receptors, and the results of the screening indicate that catechol is a surprisingly good host for chloride anions.     

Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins

The importance and utility of Ala(β) methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins is explored. Using (2)H and (13)C relaxation measurements in {U-(2)H; Ala(β)-[(13)CHD(2)]}-labeled Malate Synthase G (MSG)--an 82-kDa monomeric enzyme that contains 73 Ala(β) methyl groups--we show that the vast majority of selectively labeled Ala(β) methyls are highly ordered. A number of NMR applications used for solution studies of structure and dynamics of large protein molecules can benefit from proximity of Ala(β) methyls to the protein backbone and their high degree of ordering. In the case of MSG, these applications include the measurement of (1)H-(13)C residual dipolar couplings in Ala(β) methyls, characterization of slow (μs-to-ms) dynamics at the substrates' binding sites, and methyl-TROSY-based NOE spectroscopy performed on {U-(2)H; Ala(β)-[(13)CH(3)]; Ile(δ1)-[(13)CH(3)]; Leu,Val-[(13)CH(3)/(12)CD(3)]}-labeled samples where the number of methyl probes for derivation of distance restraints is maximized compared to the state-of-the-art ILV labeling methodology.