Hai-Bo Yi

Interaction of Benzene with Transition Metal Cations: Theoretical Study of Structures, Energies, and IR Spectra.

The cation-π interactions have been intensively studied. Nevertheless, the interactions of π systems with heavy transition metals and their accurate conformations are not well understood. Here, we theoretically investigate the structures and binding characteristics of transition metal (TM) cations including novel metal cations (TM(n+) = Cu(+), Ag(+), Au(+), Pd(2+), Pt(2+), and Hg(2+)) interacting with benzene (Bz). For comparison, the alkali metal complex of Na(+)-Bz is also included. We employ density functional theory (DFT) and high levels of ab initio theory including Møller-Plesset second-order perturbation (MP2) theory, quadratic CI method with single and double substitutions (QCISD), and the coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). Each of the transition metal complexes of benzene exhibits intriguing binding characteristics, different from the typical cation-π interactions between alkali metal cations and aromatic rings. The complexes of Na(+), Cu(+), and Ag(+) favor the conformation of C6v symmetry with the cation above the benzene centroid (πcen). The formation of these complexes is attributed to the electrostatic interaction, while the magnitude of charge transfer has little correlation with the total interaction energy. Because of the TM(n+)←π donation, cations Au(+), Pd(2+), Pt(2+), and Hg(2+) prefer the off-center π conformation (πoff) or the π coordination to a C atom of the benzene. Although the electrostatic interaction is still important, the TM←π donation effect is responsible for the binding site. The TM(n+)-Bz complexes give some characteristic IR peaks. The complexes of Na(+), Cu(+), and Ag(+) give two IR active modes between 800 and 1000 cm(-1),which are inactive in the pure benzene. The complexes of Au(+), Pd(2+), Pt(2+), and Hg(2+) give characteristic peaks for the ring distortion, C-C stretching, and C-H stretching modes as well as significant red-shifts in the CH out-of-plane bending.

Hydrates of Cu2+ and CuCl+ in dilute aqueous solution: a density functional theory and polarized continuum model investigation.

In this work, structures, and properties of Cu(2+) and CuCl(+) hydrates in the gas and aqueous phases have been investigated using the B3LYP method. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) were both taken into account for CuCl(+) hydrates. Our calculations show that [Cu(H(2)O)(n)](2+) clusters favor a very open four-coordinated structure for n = 5-12 in the gas phase, while a five-coordinated conformer is favored for n > or = 8 in the aqueous phase. An approximate complete solvation shell of Cu(2+) in the aqueous phase needs more than 12 water molecules, while that of CuCl(+) in the aqueous phase needs only about eight water molecules. For [CuCl(H(2)O)(n)](+) clusters, the most stable structure is a four-coordinated CIP conformer for n = 4-7 in the gas phase and a five-coordinated CIP conformer for n = 8-10 in the aqueous phase. However, the five-coordinated CIP/h conformer (CIP conformer that the axial chloride atom tends to dissociate) of [CuCl(H(2)O)(n)](+) clusters becomes more favorable as n increases to 11. As the hydration process proceeds, the charges on the copper atom of [Cu(H(2)O)(n)](2+) clusters decrease, while those of [CuCl(H(2)O)(n)](+) clusters increase (probably due to the dissociation of Cl(-)). The d-d electron transition and partial charge transition band around 160 nm of the five-coordinated conformer of [Cu(H(2)O)(n)](2+) clusters and those bands (approximately 170 and approximately 160 nm) of SSIP or five-coordinated CIP/h conformers of [CuCl(H(2)O)(n)](+) clusters are coincident with the absorption of [Cu](2+)(aq) species (approximately 180 nm) resolved from the spectra obtained in trace CuCl(2) (ca. 10(-5) mol x kg(-1)) + LiCl (0-18 mol x kg(-1)) aqueous solution, while those of five-coordinated CIP conformers of [CuCl(H(2)O)(n)](+) clusters (n = 8 and 9) around 261 and 247 nm correspond to the absorption of [CuCl](+)(aq) species (approximately 250 nm). Our calculated electronic spectra indicate that the typical peak of copper(II)-chloride complexes changes from 180 to 250 nm, and 275 nm, as the process of Cl(-) coordination. For [Cu](2+)(aq), [CuCl](+)(aq), and [CuCl(2)](0)(aq) species, the central Cu(II) atom prefers five-coordination.

Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity

G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking activity, which has been widely employed in multidisciplinary fields. However, its further applications are hampered by its relatively weak activity compared with protein enzymes. Herein, we report a unique intramolecular enhancement effect of the adjacent adenine (EnEAA) at 3′ end of G4 core sequences that significantly improves the activity of G4 DNAzymes. Through detailed investigations of the EnEAA, the added 3′ adenine was proved to accelerate the compound I formation in catalytic cycle and thus improve the G4 DNAzyme activity. EnEAA was found to be highly dependent on the unprotonated state of the N1 of adenine, substantiating that adenine might function as a general acid–base catalyst. Further adenine analogs analysis supported that both N1 and exocyclic 6-amino groups in adenine played key role in the catalysis. Moreover, we proved that EnEAA was generally applicable for various parallel G-quadruplex structures and even G4 RNAzyme. Our studies implied that adenine might act analogously as the distal histidine in protein peroxidases, which shed light on the fundamental understanding and rational design of G4 DNAzyme/RNAzyme catalysts with enhanced functions.

[CuCl3]− and [CuCl4]2− Hydrates in Concentrated Aqueous Solution: A Density Functional Theory and ab Initio Study

In this work, structures and thermodynamic properties of [CuCl(3)](-) and [CuCl(4)](2-) hydrates in aqueous solution were investigated using density functional theory and ab initio methods. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) structures were both taken into account. Our calculations suggest that [CuCl(3)(H(2)O)(n)](-) clusters might favor a four-coordinated CIP structure with a water molecule coordinating with the copper atom in the equatorial position for n = 3 and 4 in aqueous solution, whereas the four-coordinated SSIP structure with one chloride atom dissociated becomes more stable as n increases to 5. For the [CuCl(4)](2-) cluster, the four-coordinated tetrahedron structure is more stable than the square-planar one, whereas for [CuCl(4)(H(2)O)(n)](2-) (n ≥ 1) clusters, it seems that four-coordinated SSIP structures are slightly more favorable than CIP structures. Our calculations suggest that Cu(2+) perhaps prefers a coordination number of 4 in CuCl(2) aqueous solution with high Cl(-) concentrations. In addition, natural bond orbital (NBO) calculations suggest that there is obvious charge transfer (CT) between copper and chloride atoms in [CuCl(x)](2-x) (x = 1-4) clusters. However, compared with that in the [CuCl(2)](0) cluster, the CT between the copper and chloride atoms in [CuCl(3)](-) and [CuCl(4)](2-) clusters becomes negligible as the number of attached redundant Cl(-) ions increases. This implies that the coordination ability of Cl(-) is greatly weakened for [CuCl(3)](-) and [CuCl(4)](2-) clusters. Electronic absorption spectra of these different hydrates were obtained using long-range-corrected time-dependent density functional theory. The calculated electronic transition bands of the four-coordinated CIP conformer of [CuCl(3)(H(2)O)(n)](-) for n = 3 and 4 are coincident with the absorption of [CuCl(3)](-)(aq) species (∼284 and 384 nm) resolved from UV spectra obtained in CuCl(2) (ca. 10(-4) mol·kg(-1)) + LiCl (>10 mol·kg(-1)) solutions, whereas the calculated bands of [CuCl(3)(H(2)O)(n)](-) in their most stable configurations are not when n = 0 - 2 or n > 4, which means that the species [CuCl(3)](-)(aq) exists in those CuCl(2) aqueous solutions in which the water activity is neither too low nor too high. The calculated bands of [CuCl(4)(H(2)O)(n)](2-) clusters correspond to the absorption spectra (∼270 and 370 nm) derived from UV measurements only when n = 0, which suggests that [CuCl(4)](2-)(aq) species probably exist in environments in which the water activity is quite low.

Hydrates of Copper Dichloride in Aqueous Solution: A Density Functional Theory and Polarized Continuum Model Investigation

In this work, the hydrates of copper dichloride in gas and aqueous phase have been investigated using the B3LYP method. Low-lying conformers of CuCl(2)(H(2)O)(n) clusters for n = 1-10 were obtained by an extensive conformation search. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) with one dissociated chloride atom (SSIP/s) and SSIP with two dissociated chloride atoms (SSIP/d) all were considered. Our calculations present such a trend that a four-fold CIP conformer is more favorable for CuCl(2)(H(2)O)(n) cluster (n < or = 7) and four-fold SSIP/s for n = 8-10 in the gas phase, while in aqueous solution, more stable structures are five-fold SSIP/s conformer for n = 7-9 and four-fold CIP conformer for n = 2-6. Hydrogen bond (HB) plays an important role in the CuCl(2) solvation, especially HBs formed between the first and second solvation shell water molecules. Electronic absorption spectra of CuCl(2)(H(2)O)(n) clusters were obtained using long-range-corrected time-dependent density functional theory. The calculated electronic absorption peak around 270 nm of CIP conformers is coincident with the absorption of [CuCl(2)](0)(aq) species resolved from the spectra obtained in solutions of trace CuCl(2) (ca. 10(-5) mol/kg) + LiCl (0-18 m), while those of SSIP/s (approximately 250 nm) and SSIP/d (approximately 180 nm) conformers probably correspond to the absorption spectra of [CuCl](+)(aq) and [Cu](2+)(aq) species, respectively. Natural bond orbital charge population analyses show that charge transfer (CT) between a central copper(II) atom and ligands (Cl and H(2)O) increases as the hydrated cluster expands, especially CT from Cu(2+) to the first solvation shell, which enhances the strength of HBs. Such CT becomes more apparent for SSIP structure with the dissociation of chloride ion. OH stretching vibration frequencies of proton donor type water in CuCl(2)(H(2)O)(n) clusters are obviously red-shifted in comparison to those of water clusters, due to CT between the central atom Cu and ligands. SSIP conformers have apparent IR absorption peaks of OH stretching vibration at approximately 3000 cm(-1) for the effect of half-dissociated chloride atoms.

Cesium-Catalyzed Regioselective Synthesis of Trisubstituted Heteroatom Alkenes: A New Strategy for the Preparation of Functional Alkenes

A highly chemo-, regio-, and stereoselective method for the synthesis of (Z)-vinylic selenosulfides and (Z)-vinylic tellurosulfides in a one-pot reaction of terminal alkynes, diaryl disulfides, and diaryl diselenides (ditellurides) catalyzed by simple base cesium hydroxide monohydrate is described. Due to the different activities of the carbon-chalcogen bonds, the target products cleave selectively and act as a kind of readily available platform molecule for the synthesis of tetrasubstituted alkenes. The mechanism of thioselenation was studied by experimental and theoretical methods.

Ionic solvation and association in LiCl aqueous solution: a density functional theory, polarised continuum model and molecular dynamics investigation

In this work, the ionic solvation and association behaviours in the LiCl aqueous solution were investigated using density functional theory (DFT), a polarised continuum model and classical molecular dynamics simulations. DFT calculations of LiCl(H2O)1–6,8 clusters show that contact ion pair (CIP) and solvent-shared ion pair (SSIP) conformers of LiCl(H2O)n (n ≥ 4) clusters are generally energetic both in the gas phase and in the aqueous solution. Some SSIP conformers may be slightly more stable than their CIP isomers when at least eight water molecules are incorporated in the inner hydration shells of LiCl hydrates. The transformation between CIP and SSIP conformers is easy by overcoming a small energy barrier, which mainly results from the hydration shell reorganisation of Li+. Molecular dynamics simulations show that ion pairs or ion clusters can be found in the LiCl aqueous solution, and the probability of CIP conformers or ion clusters presented in the LiCl solution generally increases with rise in temperature. However, the presentation of ion pairs or ion clusters in the LiCl aqueous solution does not inevitably lead to the nucleation of LiCl crystallisation.

Hydration characteristics of Ca2+ and Mg2+: a density functional theory, polarized continuum model and molecular dynamics investigation

In this work, density functional theory, Møller–Plesset second-order perturbation theory, and ab initio molecular dynamics (AIMD) were used to investigate hydrated characteristics of Mg2+ and Ca2+ as a function of coordination number in the first hydration shell (CN) and cluster size. It is generally accepted that the CNs of Mg2+ and Ca2+ are both six. Calculations show that the hydration of Mg2+ generally prefers six-coordinated structures, whereas the CN value of Ca2+ varies from 6 to 8 as the hydration proceeds. Moreover, the first hydration of Ca2+ is found to be more flexible than that of Mg2+, as indicated by the results of transition state calculations and AIMD simulations. In addition, the constraint of Mg2+ on the first hydration shell is obviously stronger than that of Ca2+, while the constraint on the inner hydration shells fades slightly faster for Mg2+ than Ca2+. It is also found that the charge transfer from central cation to water molecules is affected only by the first hydration shell for Mg2+, whereas by the first and second hydration shells for Ca2+. Based on hydration characteristics, approximatively saturated ion hydration shells for the hydration of Mg2+ and Ca2+ were proposed.

Theoretical study of photoinduced electron transfer from tetramethylethylene to tetracyanoethylene

Using ab initio and density functional calculations, we studied photoexcitation of a charge-balanced electron donor–acceptor (DA) complex comprised of tetracyanoethylene (TCE) and tetramethylethylene (TME). We considered both the TCE-TME stacked conformer and a possible conformer with a solvent molecule (dichloromethane) inserted between TCE and TME. The photoexcitation of the DA complex can directly form a charge transfer (CT) state. Our theoretical investigations show that the CT state can also be produced from the decay of higher excited states. Using the continuum model, we investigated the solvent effects on CT absorption, local excitation, and CT emission in the polar solvent. The equilibrium solvation energies of the ground and excited states of the DA complex were calculated using the self-consistent reaction field method, and then the correction of nonequilibrium solvation energies for the vertical transitions was made. The transition energies (i.e., CT absorption for the DA complexes and CT emis...

DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores

Abstract Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583−668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.