Homogeneous Dimers Research Articles

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions

We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).

Effects of Heterogeneity in Small π-Type Dimers: Homogeneous and Mixed Dimers of Diacetylene and Cyanogen.

The homo- and heterogeneous dimers of diacetylene (H-C≡C-C≡C-H) and cyanogen (N≡C-C≡N) were studied using ab initio electronic structure computations to probe the effects of heterogeneity on noncovalent interactions between systems with delocalized π electron networks. Full geometry optimizations and harmonic vibrational frequencies were performed using the robust coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) method with the triple-ζ plus 2 sets of polarization functions TZ2P(f,d)++ basis set. Seven basic configurations were examined for each dimer (cross, stacked, parallel-slipped, parallel-tipped, linear, T-shaped and Y-shaped), but only four stationary points were identified on the potential energy surfaces (PESs) of the homogeneous cyanogen dimer and the mixed diacetylene/cyanogen dimer. Six previously characterized stationary points on the diacetylene dimer PES were re-examined with the CCSD(T) method and the TZ2P(f,d)++ basis set for consistency. Second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) complete basis set (CBS) limit interaction energies were estimated using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods in conjunction with the VQZ-F12 basis set. On the cyanogen dimer PES, the C2v T-shaped structure is the only minimum, with an average electronic interaction energy, Eint, of -1.96 kcal mol(-1) at the CCSD(T) CBS limit. The Cs Y-shaped structure (in agreement with previous results) is the global minimum on the diacetylene dimer PES, having a mean CCSD(T) CBS limit Eint of -1.75 kcal mol(-1). Three low-lying minima have been identified on the diacetylene/cyanogen dimer PES, a C∞v linear, a C2v cross, and a Cs parallel-slipped structure with average CCSD(T) CBS limit interaction energies of -2.00, -2.16, and -2.45 kcal mol(-1), respectively.

Research of dimer diffusion and dissociation on Cu surfaces

In this paper, we use molecular dynamics simulation to analyze the diffusion and dissociation barriers of homogeneous (Cu2) and heterogeneous dimer (Ag2, Pd2) on the surface of Cu(100), (111) surface. We explore the diffusion and dissociation process and characteristics of those dimers on Cu surface and compare their diffusion and dissociation barriers of dimer, the binding energies of the dimer and substrate, substrate surface textures, temperatures, etc. The semiempirical EAM potential is used in the simulation.

Accurate Interaction Energies for Problematic Dispersion-Bound Complexes: Homogeneous Dimers of NCCN, P2, and PCCP.

All intermolecular interactions involve London dispersion forces. The accurate treatment of dispersion is essential for the computation of realistic interaction potentials. In general, the most reliable method for computing intermolecular interactions is coupled-cluster singles and doubles with perturbative triples [CCSD(T)] in conjunction with a sufficiently flexible Gaussian atomic orbital basis set, a combination which is not routinely applicable due to its excessive computational demands (CPU time, memory, storage). Recently, many theoretical methods have been developed that attempt to account for dispersion in a more efficient manner. It is well-known that dispersion interactions are more difficult to compute in some systems than others; for example, π-π dispersion is notoriously difficult, while alkane-alkane dispersion is relatively simple to compute. In this work, numerous theoretical methods are tested for their ability to compute reliable interaction energies in particularly challenging systems, namely, the P2, PCCP, and NCCN dimers. Symmetry-adapted perturbation theory (SAPT) is applied to these dimers to demonstrate their sensitivity to the treatment of dispersion. Due to the small size of these systems, highly accurate CCSD(T) potential energy curves could be estimated at the complete basis set limit. Numerous theoretical methods are tested against the reliable CCSD(T) benchmarks. Methods using a treatment of dispersion that relies on time-dependent density functional theory (TDDFT) response functions are found to be the most reliable.

Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking

We determined the size and shape of full-length avian sarcoma virus (ASV) integrase (IN) monomers and dimers in solution using small angle x-ray scattering. The low resolution data obtained establish constraints for the relative arrangements of the three component domains in both forms. Domain organization within the small angle x-ray envelopes was determined by combining available atomic resolution data for individual domains with results from cross-linking coupled with mass spectrometry. The full-length dimer architecture so revealed is unequivocally different from that proposed from x-ray crystallographic analyses of two-domain fragments, in which interactions between the catalytic core domains play a prominent role. Core-core interactions are detected only in cross-linked IN tetramers and are required for concerted integration. The solution dimer is stabilized by C-terminal domain (CTD-CTD) interactions and by interactions of the N-terminal domain in one subunit with the core and CTD in the second subunit. These results suggest a pathway for formation of functional IN-DNA complexes that has not previously been considered and possible strategies for preventing such assembly.

Molecular Engineering of a Secreted, Highly Homogeneous, and Neurotoxic Aβ Dimer

Aβ oligomers play a key role in the pathophysiology of Alzheimer's disease. Research into structure-function relationships of Aβ oligomers has been hampered by the lack of large amounts of homogeneous and stable material. Using computational chemistry, we designed conservative cysteine substitutions in Aβ aiming at accelerating and stabilizing assembly of Aβ dimers by an intermolecular disulfide bond without changing its folding. Molecular dynamics simulations suggested that mutants AβS8C and AβM35C exhibited structural properties similar to those of Aβ wildtype dimers. Full length, mutant APP was stably expressed in transfected cell lines to study assembly of Aβ oligomers in the physiological, secretory pathway and to avoid artifacts resulting from simultaneous in vitro oxidation and aggregation. Biochemical and neurophysiological analysis of supernatants indicated that AβS8C generated an exclusive, homogeneous, and neurotoxic dimer, whereas AβM35C assembled into dimers, tetramers, and higher oligomers. Thus, molecular engineering enabled generation of bioactive, homogeneous, and correctly processed Aβ dimers in vivo.

Homogeneous catalytic dimerization of propylene with bis(imino)pyridine vanadium(III) complexes

Abstract A series of new bis(imino)pyridine vanadium(III) complexes was synthesized. They were tested for the homogeneous catalytic dimerization of propylene after activation with MAO. The activity and selectivity depend on the ligand structure of the corresponding organic coordination compound. The influence of PPh 3 as an additive was investigated and high dependency could be observed.

Are sp Lithiated Carbons More Nucleophilic than sp2 or sp3 Ones? A Comparative DFT Study of the Condensation of Propynyllithium Aggregates on Formaldehyde

The interaction between 1-propynyllithium, taken as a model of sp organolithium compound, and formaldehyde has been investigated with DFT theoretical methods. The unsolvated monomer, homogeneous dimer, trimer, tetramer, and hexamer have been considered, as well as the mixed aggregates with lithium dimethylamide in various oligomeric forms. In most cases, the separate entities, their docking complexes, the transition states, and the condensation products have been characterized. Overall, the general reaction scheme remains the same whatever the hybridization and the aggregation. However, the dimeric sp nucleophiles are expected to be more reactive (at least in kinetic conditions), while monomeric sp(3) entities would be the best nucleophiles in kinetic and thermodynamic conditions, even if its docking is the least exothermic. This work also suggests that the aggregation plays a relatively limited role on the model reaction.

Photoelectron spectroscopy of homogeneous nucleic acid base dimer anions

We report the photoelectron spectra of homogeneous dimer anions of the nucleobases: uracil, thymine, cytosine, adenine, and guanine, i.e., U(2)(-), T(2)(-), C(2)(-), A(2)(-), and G(2)(-) along with DFT calculations on U(2)(-) and T(2)(-). Based on these calculations the photoelectron spectrum of T(2)(-) was assigned as being due to both a proton transferred and a non-proton transferred isomer, while the photoelectron spectrum of U(2)(-) was assigned in terms of a single dominant barrier-free proton transferred isomer. Photoelectron spectra were also measured with a different source and on a different type of photoelectron spectrometer for U(2)(-), T(2)(-), A(2)(-), (1-MeT)(2)(-) and (1,3-Me(2)U)(2)(-).

Axial Ligand Exchange Reactions ofmeso-Aryl Subporphyrins—Axially Fluoro-Substituted Subporphyrin and a μ-Oxo Dimer and Trimer of Subporphyrins

High reactivity of the boron atom of meso-aryl subporphyrins enables the introduction of a broad range of functional groups to its axial position. Axially fluoro-substituted subporphyrins were easily synthesized upon treatment of axially hydroxyl-substituted subporphyrins with BF(3).OEt(2). Homogeneous mu-oxo dimers of subporphyrins were formed by heating monomers in the presence of triethylamine under a high vacuum. A heterogeneous subporphyrin-phthalocyanine-subporphyrin trimer was selectively formed from the respective monomers under similar reaction conditions. Structures of these molecules were elucidated by (1)H NMR spectra and a single-crystal X-ray diffraction analysis, and the interactions between neighboring chromophores in the dimeric systems were estimated from absorption and magnetic circular dichroism spectra.

Homogeneous gold-catalyzed efficient oxidative dimerization of propargylic acetates

A highly efficient gold-catalyzed oxidative dimerization of propargylic acetates is developed. In this chemistry, Selectfluor oxidation of Au(I) to Au(III) is readily incorporated into Au-catalyzed tandem reactions of propargylic acetates, and transmetallation and reductive elimination on Au(III) intermediates are likely involved.

Aldehyde C–H activation with late transition metal organometallic compounds. Formation and reactivity of acyl hydrido complexes

This perspective focuses on the aldehyde C-H activation promoted by late transition metals, including the chelation-assisted reactions. The mechanisms currently accepted for different metal complexes, the reactivity of acyl hydrido species formed, and the reactions promoted on further aldehyde when using excess reagent are discussed. Homogeneous catalytic aldehyde decarbonylation or dimerization reactions are also reviewed.

A highly active histidine-tagged Chlamydomonas reinhardtii Photosystem II preparation for structural and biophysical analysis

We describe a genetically engineered strain of Chlamydomonas reinhardtii where the PsbH subunit of Photosystem II (PSII) has been modified to include a C-terminal polyhistidine tag. The strain was generated by the rescue to photoautotrophic growth of a psbH insertional mutant following chloroplast transformation with the modified gene. This selection strategy confirms that the addition of the tag to PsbH does not prevent the assembly of functional PSII, and results in an engineered strain with tagged PSII but no antibiotic-resistance markers in the chloroplast genome. Consequently, the strain is suitable for subsequent genetic manipulation of chloroplast PSII genes. We also describe a rapid PSII isolation procedure that gives a preparation capable of high rates of oxygen evolution. This preparation is suitable for spectroscopic analysis as shown by EPR analysis of the S2 state of the water oxidation cycle. Furthermore, electron microscopy, coupled to single particle analysis, has revealed the isolated PSII to be structurally homogeneous core dimers that are ideally suited for higher resolution structural studies.

Potential energy surfaces for small alcohol dimers. II. Propanol, isopropanol, t-butanol, and sec-butanol

Potential energy landscapes for homogeneous dimers of propanol, isopropanol, tert-butanol, and sec-butanol were obtained using 735 counterpoise-corrected energies at the MP2/6-311+G(2df,2pd) level. The landscapes were sampled at 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of the yaw, pitch, and roll of one monomer relative to the other and the spherical angles between the two monomer centers (taken as the C atom attached to the O). The resultant individual energy surfaces and their complex topographies were also regressed using a site-site pair potential model using a modified Morse potential that provides a mathematically simple representation of the landscapes suitable for use in molecular simulations. Generalized Morse parameters were also obtained for this model from a composite regression of these energy landscapes and those previously reported for methanol and ethanol. The quality of fit for all these energy landscapes suggests that these site parameters have transferability for possible use on other alcohols.

Potential energy surfaces for small alcohol dimers I: Methanol and ethanol

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP26-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular simulations. A modified Morse potential is used for the individual pair interactions either with or without point charges to represent the monomer charge distribution. A slightly better representation of the methanol landscape is obtained using point charges, while the potential energy landscape of ethanol is slightly better without point charges. This latter representation may be computationally advantageous for molecular simulations because it avoids difficulties associated with long-range effects of point-charge-type models.

Gas phase infrared multiple-photon dissociation spectra of methanol, ethanol and propanol proton-bound dimers, protonated propanol and the propanol/water proton-bound dimer

The infrared multiphoton dissociation (IRMPD) spectra of three homogenous proton-bound dimers are presented and the major features are assigned based on comparisons with the neutral alcohol and with density functional theory calculations. As well, the IRMPD spectra of protonated propanol and the propanol/water proton-bound dimer (or singly hydrated protonated propanol) are presented and analysed. Two primary IRMPD photoproducts were observed for each of the alcohol proton bound dimers and were found to vary with the frequency of the radiation impinging upon the ions. For example, when the proton-bound dimer absorbs weakly a larger amount of S(N)2 product, protonated ether and water, are observed. When the proton-bound dimer absorbs more strongly, an increase in the simple dissociation product, protonated alcohol and neutral alcohol, is observed. With the aid of RRKM calculations this frequency dependence of the branching ratio is explained by assuming that photon absorption is faster than dissociation for these species and that only a few photons extra are necessary to make the higher-energy dissociation channel (simple cleavage) competitive with the lower energy (S(N)2) reaction channel.

A DFT Theoretical Study of the Condensation of Aggregates of sp2 Organolithium Compounds on Formaldehyde

[Chemical reaction: See text] The interaction between three different sp2 organolithium compounds (vinyllithium, 2-methoxyvinyllithium and phenyllithium) and formaldehyde has been investigated using DFT theoretical methods. The unsolvated monomers and dimers have been considered and compared to the 1:1 mixed aggregates formed with lithium dimethylamide. In all cases, the separate entities, their docking complexes, the transition states, and the condensation products have been characterized and compared to the corresponding situations involving methyllithium, taken as a prototypic sp3 nucleophile. Regarding the monomers, this study shows that, in the three cases considered, formaldehyde forms a pretransition state complex in which the oxygen of the carbonyl interacts with the lithium cation along one of its lone pair. A small energy barrier (< or =2.1 kcal.mol(-1)) brings to the transition state, then to the lithium alcoholate resulting from the largely exothermic condensation (approximately 40 kcal.mol(-1)). The structure of the homogeneous dimers considered in a second step has been optimized and lead to arrangements in which a planar quadrilateral C-Li-C-Li is always obtained. In the presence of formaldehyde, these entities provide complexes exhibiting lithium-oxygen interaction similar to those occurring with the monomers. For the dimers, the geometry at the TS evokes a pi-complex between the C=O and the lithium cation, particularly pronounced in the case of phenyllithium. The resulting alcoholates are obtained following a larger exothermic reaction (approximately 55 kcal.mol(-1)). The heterogeneous dimers with lithium dimethylamide have been finally examined. In these cases, the aldehyde can orientate toward either the carbon or the nitrogen, leading to the expected lithium alcoholate or alpha-amino alcoholate, respectively. Whatever the orientation, the complexes present characteristics close to those calculated for the homogeneous dimer complexes. These similarities are conserved at the transition state.

Infrared spectra of homogeneous and heterogeneous proton-bound dimers in the gas phase

Infrared multiphoton dissociation spectra of three homogeneous and two heterogeneous proton-bound dimers were recorded in the gas phase. Comparison of the experimental infrared spectra recorded in the fingerprint region of the proton-bound dimers with spectra predicted by electronic structure calculations shows that all modes which are observed contain motion of the proton oscillating between the two monomers. The O-H-O asymmetric stretch for the homogeneous dimers is shown to occur at around 800 cm-1. As expected, the O-H-O asymmetric stretching modes for the heterogeneous proton-bound dimers are observed to shift to significantly higher energy with respect to those for the homogeneous proton-bound dimers due to the asymmetry of the O-H-O moeity. This shift is shown to be predictable from the difference in proton affinities between the two monomers. Density functional predictions of the infrared spectra based on the harmonic oscillator model are demonstrated to predict the observed spectra of the homogeneous proton-bound dimers with reasonable accuracy. Calculations of the structure and infrared spectrum of protonated diglyme at the B3LYP/6-31+G** level and basis also agree well with an infrared spectrum recorded previously. For both heterogeneous proton-bound dimers, however, the predicted spectra are blue-shifted with respect to experiment.

Antigen binding and stability properties of non-covalently linked anti-CD22 single-chain Fv dimers

By varying linker length and domain orientation three multivalent derivatives of a monovalent anti-CD22 single-chain fragment variable (scFv) antibody were generated. Shortening the linker of the V H–V L oriented scFv to 5 or 0 residues resulted in the formation of diabodies or a mixture of tetramers and trimers, respectively. Unexpectedly, a V L–0–V H scFv assembled to homogenous dimers, remained substantially more stable than the V H–5–V L diabody when incubated in human serum at 37 °C, and retained its dimeric state when concentrated up to 4 mg/ml. These properties suggest the V L–0–V H scFv could become an attractive vehicle for the selective delivery of multiple effector molecules to CD22 + tumor cells.

Molecular structure and electrochemical properties of alkyldithiocarbamates

Cyclic voltammetry, chronoamperometry, chronocoulometry and rotating disc electrode techniques have been used to study redox properties of dithiocarbamate lithium salts solutes in 0.1 M LiClO 4/DMSO solution. The investigated compounds have been synthesized from N, N′-dimethylethylenediamine to which one or two dithiocarbonyl groups were attached by a reaction with CS 2 in an alkaline solution. Voltammetric studies of the oxidation of these moieties showed the irreversible, though reproducible, broad peak at scan rates ranging from 0.01 to 0.5 V s −1. The chronoamperometric and rotating disc electrode experiments confirmed the consumption of 1e/active group. Upon changing the electrode from Pt to glassy carbon only slight shift of the anodic peak potential, and negligible current change has been observed. These findings are interpreted as an indication that the electrode materials do not participate directly in the dithiocarbamate radicals formation (for example, via chemisorption) and in further dimerization of the radicals to thiuram disulfide. The latter process is assumed to proceed at the rate close to the diffusion limit. The calculated symmetry coefficient are distinctly lower than 0.5, the value predicted by the Butler–Volmer theory. Such an outcome implies that the potential range where the reaction proceeds is much more positive than the standard potential of the reaction. The oxidation of the compound containing two electroactive groups has led to the formation of a wide spectrum of diverse disulfide compounds differing one from another by the molecular weight (diffusion coefficient) owing to the various degree of the coupling. The semi-empirical quantum-chemical calculations showed the structure reorganization of the dithiocarbamate anions upon electron detachment enforced by localization of the unpaired electron on the sulfur atoms. It may favour kinetically the formation of thiuram disulfide through the fast homogeneous dimerization of the dithiocarbamate radicals.