Comparative DFT study of van der Waals complexes: rare-gas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers

Recent interest in the application of density functional theory prompted us to test various functionals for the van der Waals interactions in the rare-gas dimers, the alkaline-earth metal dimers, zinc dimer, and zinc-rare-gas dimers. In the present study, we report such tests for 18 DFT functionals, including both some very recent functionals and some well-established older ones. We draw the following conclusions based on the mean errors in binding energies and complex geometries: (1) B97-1 gives the best performance for predicting the geometry of rare-gas dimers, whereas M05-2X and B97-1 give the best energetics for rare-gas dimers. (2) PWB6K gives the best performance for the prediction of the geometry of the alkaline-earth metal dimers, zinc dimers, and zinc-rare-gas dimers. M05-2X gives the best energetics for the metal dimers, whereas B97-1 gives the best energetics for the zinc-rare-gas dimers. (3) The M05 functional is unique in providing good accuracy for both covalent transition-metal dimers and van der Waals metal dimers. (4) The combined mean percentage unsigned error in geometries and energetics shows that M05-2X and MPWB1K are the overall best methods for the prediction of van der Waals interactions in metal and rare-gas van der Waals dimers.     

Hydrogen desorption kinetics from the Si(1-x)Gex(100)-(2x1) surface

We study the influence of germanium atoms upon molecular hydrogen desorption energetics using density functional cluster calculations. A three-dimer cluster is used to model the Si((1-x))Ge(x)(100)-(2x1) surface. The relative stabilities of the various monohydride and clean surface configurations are computed. We also compute the energy barriers for desorption from silicon, germanium, and mixed dimers with various neighboring configurations of silicon and germanium atoms. Our results indicate that there are two desorption channels from mixed dimers, one with an energy barrier close to that for desorption from germanium dimers and one with an energy barrier close to that for desorption from silicon dimers. Coupled with the preferential formation of mixed dimers over silicon or germanium dimers on the surface, our results suggest that the low barrier mixed dimer channel plays an important role in hydrogen desorption from silicon-germanium surfaces. A simple kinetics model is used to show that reasonable thermal desorption spectra result from incorporating this channel into the mechanism for hydrogen desorption. Our results help to resolve the discrepancy between the surface germanium coverage found from thermal desorption spectra analysis, and the results of composition measurements using photoemission experiments. We also find from our cluster calculations that germanium dimers exert little influence upon the hydrogen desorption barriers of neighboring silicon or germanium dimers. However, a relatively larger effect upon the desorption barrier is observed in our calculations when germanium atoms are present in the second layer.     

Role of hydrogen in dimerizaton of aluminum clusters: a theoretical study

We have used density functional theory to investigate how Al(13) cluster dimers can be formed with or without a bridging hydrogen. We have identified several stable dimers in which 0, 1, or 2 hydrogen atoms link two bare clusters together. Each of these structures can adsorb further H atoms in atop sites on the surface of the dimer. Additional dimers were identified with 3 and 4 H atoms linking the clusters but these are only stable in the multihydrogenated form. Reaction profiles for the formation of these dimers from a range of cluster and H atom combinations indicate that the dimer structures are energetically favored over the isolated clusters. This observation may have significant implications for the design of cluster-assembled materials.     

Dimer statistics on a Bethe lattice

We discuss the exact solutions of various models of the statistics of dimer coverings of a Bethe lattice. We reproduce the well-known exact result for noninteracting hard-core dimers by both a very simple geometrical argument and a general algebraic formulation for lattice statistical problems. The algebraic formulation enables us to discuss loop corrections for finite dimensional lattices. For the Bethe lattice we also obtain the exact solution when either (a) the dimers interact via a short-range interaction or (b) the underlying lattice is anisotropic. We give the exact solution for a special limit of dimers on a Bethe lattice in a quenched random potential in which we consider the maximal covering of dimers on random clusters at site occupation probability p. Surprisingly the partition function for "maximal coverage" on the Bethe lattice is identical to that for the statistics of branched polymers when the activity for a monomer unit is set equal to -p. Finally we give an exact solution for the number of residual vacancies when hard-core dimers are randomly deposited on a one dimensional lattice.     

Symmetric bent-shaped liquid crystal dimers showing transitions between optically uniaxial and biaxial smectic phases

We report the synthesis of a new homologous series of symmetric bent-shaped liquid crystal dimers bearing oxybiphenylcarboxylate mesogens linked by a pentamethylene spacer. The dimers were characterised by optical, thermal, X-ray diffraction and computational techniques. Shorter dimers showed an I-N-SmA-SmC phase sequence with strong first-order phase transitions. For the longer dimers, the unconventional uniaxial SmA phase present in shorter members collapsed. A 9:1 binary mixture of a bent dimer with a non-mesogenic dimer exhibited upon the SmA-SmC phase transition a maximum layer contraction of 1%.     

Dimers of the higher-energy conformer of formic acid: experimental observation

We report on the first experimental observation of formic acid dimers composed of two molecules of the higher-energy cis conformer. The cis-cis formic acid dimers are prepared in an argon matrix by selective vibrational excitation of the ground state trans conformer (deuterated form HCOOD) combined with thermal annealing of the matrix at about 30 K. Five cis-cis formic acid dimers are predicted by ab initio calculations (interaction energies from -16.9 to -27.2 kJ mol(-1)), and these structures are used for the assignment of the experimental spectra. Selective vibrational excitation of the obtained cis-cis dimers leads to the formation of several trans-cis dimers, which supports the proposed assignments.     

Non-symmetric calamitic liquid crystal dimers containing troponoid and benzenoid units

Five types of non-symmetric calamitic dimers were synthesized to investigate the effect of the core structure and length of the spacer on mesomorphic properties. Two non-symmetric dimers containing a troponoid and benzenoid unit showed smectic A and C phases whereas the corresponding benzenoid dimers showed no mesophase. Non-symmetric dimers with a three-ring system showed smectic A and C phases with higher transition temperatures than the two-ring system. We propose packing models for these non-symmetric dimers by considering the direction of the dipole moments of the ring structures and microsegregation between the polar units and the non-polar chains.     

PHOTOREACTIVATION OF PYRIMIDINE DIMERS IN DNA FROM THYROID CELLS OF THE TELEOST, POECILIA FORMOSA

Abstract— We have developed and used a simple technique to estimate the quantity of pyrimidine dimers in unlabeled cellular DNA. DNA is extracted from cells, treated with an endonuclease specific for dimers, and its molecular weight estimated by its electrophoretic mobility on alkaline agarose slab gels. The technique is used to show that cells from thyroid tissue of the fish Poecilia formosa have photoreactivating activity towards dimers in the cellular DNA.     

W-shaped mesogens and variations of their molecular structure

New bent-core liquid crystalline dimers with W-shaped molecular geometry have been prepared and studied. We have modified the dimer shape by variation of the connecting part between two bent-core units and changing the terminal chains (perfluoroalkyl, siloxanealkyl). Additionally, we have altered the inner bend angle value (120°, 60° and 148°) by utilization of different aromatic units. Mesomorphic properties of new dimers were established based on the texture observation in the polarizing microscope and DSC measurements. Moreover, x-ray structural analysis has been performed for selected dimers to confirm phase identification. For most of the studied dimers, nematic or columnar phases have been detected, for several compounds appearing in a nematic-columnar phase sequence on cooling from the isotropic phase. The studied dimers showed richer polymorphism than their monomeric counterparts.     

4d transition metal monoxides,monocarbides, monoborides,mononitrides, and monofluorides: A quantum chemical study

We have studied 4d transition metal monoboride, monocarbide, mononitride, monoxide, and monofluorides using density functional method at B3LYP/LanL2Dz level. The lowest spin state, relative stability, bond length, atomic charges, electron affinity, ionization potential, binding energy, and vibrational frequencies for these dimers are obtained. The cation and anion of these dimers are also studied. The properties of these dimers are compared. It was found that the ionization potentials for these dimers are much higher than the electron affinities of these dimers. The range of electron affinities is widest for 4d transition metal monocarbides and is narrow for 4d transition metal mononitrides. The range of ionization potential is widest for 4d transition metal monoxides and is narrow for 4d transition metal monocarbides. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Extremely strong near-IR two-photon absorption in conjugated porphyrin dimers: quantitative description with three-essential-states model

Two-photon absorption spectra (2PA) of a series of conjugated dimers and the corresponding monomer were studied in the near-IR region. All of the dimers show very large peak cross section values, sigma(2) = (3-10) x 10(3) GM (1 GM = 1 x 10(-50) cm(4) s photon(-1)), which is several hundred times larger than that obtained for the corresponding monomer in the same region. We explain such dramatic cooperative enhancement by a combination of several factors, such as strong enhancement of the lowest one-photon Q-transition, better resonance conditions in the three-level system, dramatic enhancement of the excited-state singlet-singlet transition, and parallel arrangement of consecutive transitions in dimers, as compared to perpendicular arrangement in the monomer. We show that the absolute values of the 2PA cross section in these molecules are quantitatively described by a quantum-mechanical expression, derived for the three-level model. We also demonstrate the possibility of singlet oxygen generation upon one- and two-photon excitation of these dimers, which makes them particularly attractive for photodynamic therapy.     

EXCISION REPAIR OF UVR-INDUCED PYRIMIDINE DIMERS IN CORNEAL DNA

Abstract— We measured excision repair of ultraviolet radiation (UVR)-induced pyrimidine dimers in DNA of the corneal epithelium of the marsupial, Monodelphis domestica , using damage-specific nucleases from Micrococcus luteus in conjunction with agarose gel electrophoresis. We observed that 100 J ^-2 of UVR from aFS–40 sunlamp(280–400 nm) induced an average of 2.2 ± 0.2 times 10^-2 endonuclease-sensitive sites per kilobase (ESS/kb) (pyrimidine dimers) and that ∼ 50% of the dimers were repaired within 12 h after exposure. We also determined that an exposure of 400 J m^-2 was needed to induce comparable numbers of pyrimidine dimers (2.5 times 10^-2) in the DNA of skin of M. domestica in vivo . In addition, we found that 50% of the dimers were also removed from the epidermal cells of M. domestica within 12 h after exposure. A dose of 100 J m^-2 was necessary to induce similar levels of pyrimidine dimers (2.0 ± 0.2 times 10^-2) in the DNA of the cultured marsupial cell line Pt K2 ( Potorous tridactylus ).     

Accurate identification of dimers from α‐pinene oxidation using high‐resolution collision‐induced dissociation mass spectrometry

Interest in mass spectrometry of highly oxidized dimers from α‐pinene oxidation has increased in the atmospheric chemistry field. Here, we apply high‐resolution collision‐induced dissociation mass spectrometry (HR‐CID‐MS) with an atmospheric pressure ionization source to investigate in detail how α‐pinene‐derived dimers are detected and identified by MS. The resulting HR‐CID spectra and specific fragmentation patterns suggest that a large fraction of dimer ions detected in full‐scan mass spectra can be hydrogen‐bonded artifact clusters and the residual small fraction includes covalently bonded actual dimers. We also show how individual fractions of the artifact clusters and actual dimers are calculated using the HR‐CID spectra.     

Monodelphis domestica: a new animal model for studies in photodermatology

The ability to photoreverse pyrimidine dimers in DNA of the South American opossum Monodelphis domestica provides a powerful tool with which to probe the role of pyrimidine dimers in ultraviolet radiation (UVR)-induced histopathologic changes of the skin of this mammal. We have observed that post-UVR exposure to photoreactivation light not only reversed pyrimidine dimers in epidermal DNA, but also suppressed the capacity of UVR to induce macroscopic and microscopic changes in the skin of M. domestica.     

An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface

Both parallel and antiparallel alpha-helical coiled-coil dimers are common among proteins; however, biophysical scrutiny has focused almost entirely on parallel dimers. We describe the development of a model system that enables efficient and systematic analysis of hydrophobic packing between antiparallel alpha-helices. Our findings reveal significant differences in packing preferences between parallel and antiparallel coiled-coils.     

DIMER PHOTOPRODUCTS IN CYTIDYLYL-(3'-5') CYTIDINE

Abstract— When CpC is exposed to ultraviolet (u.v.) radiation, dimers are produced both photochemically and by dark reactions. A reaction scheme for the production of these dimers is presented. We have shown that a single dimer, CC₁, is initially produced photochemically. This is converted by a spontaneous reaction to a second dimer, CC₂. The dimer CC₂ may also spontaneously revert back to CC₁ and if no side reactions were involved a thermal equilibrium between these txo dimers would be established with about two to three times the concentration of CC₂, as of CC₁. The rate constants for the interconversion of these two dimers vary from about 0.05 to 0.4 hr^-1 over the pH range 2.7 to 8.4. The dimers of CpC have maximum stability near pH 7. The two dimers CC₁ and CC₂ can also be reversed to CpC by u.v. irradiation. Both these dimers in turn deaminate to dimers of UpC and then to UU. The rate constants for these deamination reactions are presented. These lie in the range 0.01 to 0.5 hr^-1 for the pH values studied. Possible structures for the two dimers are suggested.     

Influence of dimerization on the nematic-isotropic phase transition in strongly polar liquid crystals

A molecular theory of the nematic-isotropic phase transition is developed for the fluid composed of rod-like particles with large longitudinal dipoles. The equilibrium between the monomers and dimers with antiparallel dipoles is explicitly taken into account and the concentration of dimers is determined self-consistently together with the nematic order parameters. We show that for small central dipole moments the nematic-isotropic transition temperature increases with the increasing dipole. This is in accordance with the results of previous approaches. By contrast, for large values of the dipole the transition temperature decreases due to the growing concentration of dimers. This result enables one to explain the results of recent computer simulations that reveal a destabilization of the nematic phase in a system of hard rods with large central longitudinal dipoles. The temperature variation of the concentration of dimers is also analysed and the sign of the concentration discontinuity at the transition point is correlated with the qualitative influence of dimers on the transition temperature.     

THE FATE OF PYRIMIDINE DIMERS IN ULTRAVIOLET-IRRADIATED CHLAMYDOMONAS

Abstract— We have developed a chromatographic technique for the separation of ³²P-labeled pyrimidine nucleotide dimers of the form Py_pPy from ³²P-phosphate in enzymatic hydroly sates of ultraviolet-irradiated DNA. Application of this technique to ³²P-labeled Chlamydomonas reinhardii shows that ultraviolet irradiation of this organism induces pyrimidine dimers in both nuclear and chloroplast DNA. We have found no evidence that these dimers are excised from either DNA species after several hours incubation under non-photoreactivating conditions. A function has been derived to permit the pyrimidine-dimer content determined from radioactive-thymine-labeled cells to be conveniently compared to that obtained from ³²P-phosphate-labeled cells.     

Use of high-performance liquid chromatography to quantitative thymine-containing pyrimidine dimers in DNA

We have developed two high-performance liquid chromatographic systems for the measurement of pyrimidine dimers in hydrolysates of DNA. Normal-phase chromatography on an NH₂ column in methanol—ethyl acetate (3:97) at an elution rate of 2.0 ml/min allowed quantitaion of thymine-containing (thymine-thymine plus thymine-uracil) pyrimidine dimers at levels as low as 0.1% of the total radioactivity as thymine in DNA. This system was unaffected by the presence of up to 1 mg of contaminating protein (bovine serum albumin) or 40 μg of DNA in hydrolysates prepared for chromatography. Reversed-phase chromatography on a μBondapak C₁₈ column allowed measurement of thymine-thymine dimers at concentrations as low as 0.02% of the total radioactivity. With 0.1% tetrahydrofuran in wateras the solvent at a flow-rate of up to 0.6 ml/min, thymine—thymine, thymine—uracil, and uracil—uracil dimers were completely resolved. We were not able to quantitate the latter two dimeric forms, however, owing to the presence of other radioactive components of undefined origin that eluted concomitantly with the uracil-containing dimers.     

Synthetic models related to furanocoumarin-CYP 3A4 interactions. comparison of furanocoumarin, coumarin, and benzofuran dimers as potent inhibitors of CYP3A4 activity

Furanocoumarin derivatives (dimers and monomers) present in commercially available grapefruit juice have the capacity to inhibit the activity of human CYP3A4. Such interactions are believed to result from the mechanism-based inhibition of CYP3A4 activity in the intestine. The aim of this work was to synthesize and test a series of dimers with a view to determining the relationship between structure and inhibitory activity and determining whether they might make suitable probes of CYP3A4 activity. We prepared a series of furanocoumarin, coumarin, and benzofuran derivatives that have inhibitory effects on the activity of human CYP3A4. A synthetic benzofuran dimer, which is more accessible than furanocoumarin dimers, exhibited activity against CYP3A4 comparable to that of furanocoumarin dimers.