The Influence of Gap Length on Cooperativity and Rate of Association in DNA-Modified Gold Nanoparticle Aggregates

Polyvalent gold nanoparticle–DNA conjugates hybridize with complementary linker DNA strands to form aggregates that exhibit sharp dissociation curves indicative of cooperative behavior. Introducing single-stranded gaps consisting of thymidines (T₁–T₂₀) into the linker strand resulted in a decrease in the number of duplexes that dissociate cooperatively. Upon adding one base insertion (T₁) the cooperative number drops from 6.3(2) to 2.8(2) duplexes. The cooperative number then increases slightly for the T₃ gap and thereafter decreases for T₈ and T₁₀, with a slight increase again for the T₂₀ gap. As the presence of a shared condensed cation cloud has been implicated in neighboring duplex cooperativity, we measured the salt-dependent behavior of T_<i>n</i> gap-linked unmodified duplexes and the number of ions released per duplex dissociation. Interestingly, the number of cations released for the duplexes with a longer gap sequence is significantly larger than the number released for a T₁ gap-linked duplex or a nicked duplex (T₀). Overall there is a correlation between the change in condensed cation density and the dissociation entropy for the unmodified T_<i>n</i> gap-linked duplexes, and the cooperative unit for the T_<i>n</i> gap-linked GNP–DNA aggregates. Using dynamic light scattering and changes in optical absorbance, we also found that aggregation of GNP–DNA is more rapid when hybridization occurs at a nicked versus gap site, which was previously observed but attributed to slower hybridization as a result of the longer linker strand. By comparing the aggregation rate of a prehybridized GNP–DNA:T₁₀-linker complex with a completely complementary GNP–DNA and a GNP–DNA that led to a T₁₀ gap, we were able to establish that the presence of the gap, not DNA length or accessibility, caused the decrease in aggregation rate. Our results support that flexibility in aggregates decreases the rate of aggregation as well as the extent of cooperativity, which has important implications in genomic DNA detection

Reactivity of triruthenium furyne and thiophyne clusters : multiple additions of thiolato and selenolato ligands through oxidative addition of S–H and Se–H bonds

Reactions of 50-electron furyne and thiophyne clusters Ru3(CO)7(μ-H)(μ3-η2-C4H2E){μ-P(C4H3E)2}(μ-dppm) (1, 2; E = O, S) with thiols, dithiols, and benzeneselenol leads to the oxidative addition of the E–H bonds followed by concomitant elimination of the alkyne (probably as the alkene) to afford a range of new thiolato and selenolato triruthenium complexes. Addition of PhSH or iPrSH in boiling benzene affords the 48-electron clusters Ru3(CO)5(μ-SR)2{μ-P(C4H3E)2}(μ-dppm)(μ-H) (3–6; E = O, S; R = Ph, iPr) resulting from the addition of 2 equiv of thiol. In contrast, analogous reactions with 1,2-ethanedithiol and 1,3-propanedithiol yield the 50-electron clusters Ru3(CO)3{μ-S(CH2)nS)2{μ-P(C4H3E)2}(μ-dppm)(μ-H) (7–10; E = O, S; n = 2, 3), in which four S–H bonds have been activated. A similar multiple addition reaction is seen upon addition of PhSeH to 1, affording the tetraselenolato complexes Ru3(CO)4(κ1-SePh)(μ-SePh)3{μ-P(C4H3O)2}(μ-dppm)(μ-H) (11) and Ru3(CO)3(μ-SePh)4{μ-P(C4H3O)2}(μ-dppm)(μ-H) (12). Reaction of 2 with PhSeH gave the tetraselenolato complex Ru3(CO)4(κ1-SePh)(μ-SePh)3{μ-P(C4H3S)2}(μ-dppm)(μ-H) (13) together with bis(seleno)-capped Ru3(CO)5{PPh(C4H3S)2}(μ3-Se)2(μ-SePh)2(μ-dppm) (14) resulting from further cleavage of two selenium–carbon bonds and formation of a new carbon–phosphorus bond. The new clusters have been characterized by a combination of analytical and spectroscopic methods, and the molecular structures of 3, 4, 7, 8, and 11 have been determined by single-crystal X-ray diffraction studies. Complexes 7–10 are examples of 50-electron clusters containing three apparent metal–metal bonds; however, DFT calculations carried out for 7 show that the longest metal–metal interaction of 3.119 Å is actually held in place by the bridging thiolato and diphosphine ligands and does not represent a direct metal–metal bonding interaction

Revealing Silica\u27s pH-Dependent Second Harmonic Generation Response with Overcharging

Isolating the contribution of the silica in second harmonic generation (SHG) studies at the silica/water interface remains a challenge. Herein, we compare SHG intensities with previously measured zeta potentials and vibrational sum frequency generation (vSFG) intensities to deconvolute the silica contribution in the SHG measurements. Under conditions that promote overcharging, the zeta potential and the vSFG measurements follow a similar trend, however, SHG yields the opposite behaviour. The results can only be rationalized by considering a significant pH dependent increase in the silica contribution. Using a simplistic, yet physically motivated model, we demonstrate that silica can interfere either constructively or destructively with water. By computing the hyperpolarizabilities of neutral and deprotonated silica clusters with density functional theory (CAM-B3LYP/6-31+G(d,p)), we reveal that one potential source of this pH-dependent response of silica is a change in the hyperpolarizability upon the deprotonation of surface sites suggesting SHG is directly sensitive to surface charging of mineral oxides

Reactivity of Triruthenium Furyne and Thiophyne Clusters: Multiple Additions of Thiolato and Selenolato Ligands through Oxidative Addition of S–H and Se–H Bonds

Reactions of 50-electron furyne and thiophyne clusters Ru₃(CO)₇(μ-H)­(μ₃-η²-C₄H₂E)­{μ-P­(C₄H₃E)₂}­(μ-dppm) (<b>1</b>, <b>2</b>; E = O, S) with thiols, dithiols, and benzeneselenol leads to the oxidative addition of the E–H bonds followed by concomitant elimination of the alkyne (probably as the alkene) to afford a range of new thiolato and selenolato triruthenium complexes. Addition of PhSH or ⁱPrSH in boiling benzene affords the 48-electron clusters Ru₃(CO)₅(μ-SR)₂{μ-P­(C₄H₃E)₂}­(μ-dppm)­(μ-H) (<b>3</b>–<b>6</b>; E = O, S; R = Ph, ⁱPr) resulting from the addition of 2 equiv of thiol. In contrast, analogous reactions with 1,2-ethanedithiol and 1,3-propanedithiol yield the 50-electron clusters Ru₃(CO)₃{μ-S­(CH₂)_<i>n</i>S)₂{μ-P­(C₄H₃E)₂}­(μ-dppm)­(μ-H) (<b>7</b>–<b>10</b>; E = O, S; <i>n</i> = 2, 3), in which four S–H bonds have been activated. A similar multiple addition reaction is seen upon addition of PhSeH to <b>1</b>, affording the tetraselenolato complexes Ru₃(CO)₄(κ¹-SePh)­(μ-SePh)₃{μ-P­(C₄H₃O)₂}­(μ-dppm)­(μ-H) (<b>11</b>) and Ru₃(CO)₃(μ-SePh)₄{μ-P­(C₄H₃O)₂}­(μ-dppm)­(μ-H) (<b>12</b>). Reaction of <b>2</b> with PhSeH gave the tetraselenolato complex Ru₃(CO)₄(κ¹-SePh)­(μ-SePh)₃{μ-P­(C₄H₃S)₂}­(μ-dppm)­(μ-H) (<b>13</b>) together with bis­(seleno)-capped Ru₃(CO)₅{PPh­(C₄H₃S)₂}­(μ₃-Se)₂(μ-SePh)₂(μ-dppm) (<b>14</b>) resulting from further cleavage of two selenium–carbon bonds and formation of a new carbon–phosphorus bond. The new clusters have been characterized by a combination of analytical and spectroscopic methods, and the molecular structures of <b>3</b>, <b>4</b>, <b>7</b>, <b>8</b>, and <b>11</b> have been determined by single-crystal X-ray diffraction studies. Complexes <b>7</b>–<b>10</b> are examples of 50-electron clusters containing three apparent metal–metal bonds; however, DFT calculations carried out for <b>7</b> show that the longest metal–metal interaction of 3.119 Å is actually held in place by the bridging thiolato and diphosphine ligands and does not represent a direct metal–metal bonding interaction