Absorption spectroscopy of molecular trimers

Absorption properties of molecular trimers are studied within a model including a single monomer internal vibrational degree of freedom. Upon photoabsorption, three excited electronic states which are coupled excitonically are accessed. Band shapes resulting from different electronic coupling strengths and geometries are analyzed. It is shown that geometric information can be extracted from the band intensities. Taking data recorded for perylene bisimide aggregates as an example, the spectra for monomer, dimer, and trimer systems are compared.     

The stereostructure of trimers of biacetyl

Structures of two trimers of biacetyl were determined on the basis of chemical and spectroscopic evidence and the single-crystal X-ray analysis. The compounds are shown to be exo-3, endo-7-diacetyl-1- hydroxy-endo-3,5,exo-7-trimethyl-cis-2,4,6-trioxabicyclo[3.3.0]octanc (2) and 11-hydroxy-1,3,5,7,11- pentamethyl-cis-2,4,6,8-tetraoxatricyclo[3.3.3.0^3.7]undecan-9-one(3).     

Nonadditivity of interaction in water trimers

The energy of (H₂O)₃ has been calculated for 29 geometrical configurations of the trimer using the SCF LCAO MO method and extended as well as minimal basis sets of Gaussian functions. For two configurations two intermediate basis sets have also been tested. The results show the nonadditive component of the interaction energy to be small. They also indicate that fairly reliable results for the trimer can be obtained using minimal basis sets and the counterpoise method to eliminate the basis set superposition error. The nonadditive contribution to the interaction energy is shown to be mainly due to the long-range induction interaction.     

Altering the landscape of viruses and bionanoparticles

In recent years, protein-based nanoparticles or bionanoparticles (BNPs), have been used as primary building blocks to generate ornate nanomaterials for a wide-range of applications. Over the past fifty years, numerous BNPs have been chemically modified or genetically engineered to function as smart drug/gene delivery vehicles, advanced vaccine vehicles, and isolated reaction vessels for inorganic, metallic, and semi-conductive depositions. These studies have contributed invaluable insights to the expansive capabilities of these simple, yet highly robust, nanosized building materials. Here we highlight some of the recent progress in the chemical modifications of BNPs and hopefully inspire the development of many new materials in the near future.     

Selective synthesis of novel cyclic phenylazomethine trimers

Novel cyclic phenylazomethine trimers (CPAs) were synthesized in a one-step dehydration of the 4-aminobenzophenone derivatives in the presence of TiCl(4) or p-toluenesulfonic acid (PTS). The CPAs were isolated in over 90% yield under nondilute conditions. When using TiCl(4) as the dehydration agent, the induction of bulky substituents at the alpha-position of the substrate enhanced the yields of the CPAs. On the other hand, PTS served as an effective catalyst for the synthesis of the phenyl-substituted CPA. This different reactivity between TiCl(4) and PTS depends on the dehydration mechanism being dominated by a kinetic process or thermodynamic one. The obtained CPAs were confirmed by NMR, UV-vis spectra, and MM2 calculation to have only a Z conformation and a nonconjugated structure compared to the linear oligophenylazomethines (OPAs) and the aniline-capped OPAs (OPA's).     

Plasmon modes of nanosphere trimers and quadrumers

Using the plasmon hybridization method, we investigate the plasmon frequencies and optical absorption spectra of symmetric configurations of nanosphere trimers and quadrumers. Plasmon hybridization allows us to express the fundamental plasmon modes of these multinanosphere systems as linear combinations of the plasmons of individual nanospheres in a manner analogous to molecular orbital theory. We show how group theory may be used to interpret the plasmon modes of each multiparticle system as specific structure-dependent symmetric combinations of the plasmon modes of the individual nanoparticles. We compare the optical absorption spectra calculated using plasmon hybridization with the spectra obtained using finite difference time domain simulations.     

Understanding the folding rates and folding nuclei of globular proteins

The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data.     

Structure of mixed group IB metal trimers

The structures of all mixed group IB trimers have been calculated in the diatomics-in-molecules (DIM) approximation. The optimum trimer geometries correspond to bent structures in C₂ or C_2v symmetry. All trimers are bound with respect to dissociation to an atom plus a diatomic. The structures can all be characterized as having an “obtuse” structure with a bond angle greater than 60°. The structure of the trimer is controlled by the atom which forms the strongest diatomic bonds. This is confirmed by calculations on the possible linear structures. The most stable linear structure has the atom which forms the strongest diatomic bonds in the central position.     

Conformational relaxation in the excited electronic states of benzil and naphthyl

A time-resolved study of the emission from benzil and naphthyl in semi-solid glasses (e.g. alcoholic glass near the melting point) using a pulsed N₂-laser as an excitation source is reported. The emission from the relaxed excited triplet shows a growth followed by a decay. This growth provides a convincing proof of geometrical relaxation occurring in the excited states of benzil and naphthyl.     

Nonadditive effects in the mixed trimers of HCl and methanethiol

Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl-CH3SH dimer and HCl-(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl-(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.     

Understanding the folding process of synthetic polymers by small-molecule folding agents

Two acceptor containing polyimides PDI and NDI carrying pyromellitic diimide units and 1,4,5,8-naphthalene tetracarboxy diimide units, respectively, along with hexa(oxyethylene) (EO6) segments as linkers, were prepared from the corresponding dianhydrides and diamines. These polyimides were made to fold by interaction with specifically designed folding agents containing a dialkoxynaphtha-lene (DAN) donor linked to a carboxylic acid group. The alkali-metal counter-ion of the donor carboxylic acid upon complexation with the EO6 segment brings the DAN unit in the right location to induce a charge-transfer complex formation with acceptor units in the polymer backbone. This two-point interaction between the folding agent and the polymer backbone leads to a folding of the polymer chain, which was readily monitored by NMR titrations. The effect of various parameters, such as structures of the folding agent and polymer, and the solvent composition, on the folding propensities of the polymer was studied.     

Template-directed one-step synthesis of cyclic trimers by ADMET

A trifurcated template, containing three secondary dialkylammonium ion recognition sites for encirclement by a dibenzo [24]crown-8-containing acyclic diene, is used to promote acyclic diene metatheses (ADMET) catalyzed by ruthenium-alkylidene complexes, affording a cyclic trimer in 55% yield. Following this one-step, threefold ADMET reaction, the resulting cyclic trimer was isolated by preparative HPLC and characterized by NMR spectroscopy and mass spectrometry.     

A correlation study of boron dimers and trimers

We have carried out ab initio molecular orbital studies of neutral and charged boron dimers and trimers, using a large basis set. Electron correlation effects are included through the techniques of fourth order many body perturbation theory. Results for total energies, geometries, binding energies, and binary fragmentation energies are presented, and where possible compared with published results. Stabilities of the geometries considered are further studied through a vibrational-mode analysis. The ground state of B₂ is predicted to be a triplet; of B ₂ ^? , a quartet, and of B ₂ ⁺ a doublet. The ground state of B₃ is a triangular doublet, of B ₃ ^? a linear singlet and of B ₃ ⁺ a triangular singlet.     

Two pseudopolymorphs of LiCl trimers with semicubane structures

The title compounds, trichlorido(μ₃‐triethylphosphine oxide‐κ³O:O:O)tris(μ₂‐triethylphosphine oxide‐κ²O:O)trilithium(I) toluene solvate, [Li₃Cl₃(C₆H₁₅OP)₄]·C₇H₈, (I), and trichlorido(μ₃‐triethylphosphine oxide‐κ³O:O:O)tris(μ₂‐triethylphosphine oxide‐κ²O:O)trilithium(I), [Li₃Cl₃(C₆H₁₅OP)₄], (II), adopt separated semicubane structures in the solid state which are the first such structures to be reported for LiCl solvates. One triethylphosphine oxide ligand bonds via its O atom to the three Li atoms in a μ₃ manner, while the other three triethylphosphine oxide ligands bridge three Li atoms in μ₂ manners. The Cl atoms are in terminal instead of bridging positions, which is rather unusual for lithium chloride solvates.     

Bismuth triflate catalyzed Claisen rearrangement of allyl naphthyl ethers

Bismuth triflate was found to be an efficient catalyst for the Claisen rearrangement of allyl naphthyl ethers. The reaction proceeds smoothly with a catalytic amount of bismuth triflate (20 mol %) to afford the corresponding ortho-allyl naphthol in moderate to good yields in most cases.     

Electronic correlation contribution to the three-body potentials for water trimers

A number of trimers of water molecules have been computed with an extended basis set in the Hartree–Fock and in the direct CI approximations. It has been verified that the three-body interaction energy can be calculated within the Hartree–Fock method. Therefore, the correlation corrections to the Hartree–Fock level are essentially additive and do not contribute significantly to three-body effects.