Thermodynamics of forming water clusters at various temperatures and pressures by Gaussian-2, Gaussian-3, complete basis set-QB3, and complete basis set-APNO model chemistries; implications for atmospheric chemistry

The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate Delta H degrees and Delta G degrees values for neutral clusters of water, (H(2)O)(n), where n = 2-6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 x 10(14) molecules/cm(3), water trimer concentrations of 2.6 x 10(12) molecules/cm(3), tetramer concentrations of approximately 5.8 x 10(11) molecules/cm(3), and pentamer concentrations of approximately 3.5 x 10(10) molecules/cm(3) in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.     

Transformation of a kinetically controlled nematic phase of a linear polymer into one which is thermodynamically controlled via cyclization [1]

The synthesis and characterization of cyclic main chain liquid-crystalline oligomers based on 1-(4-hydroxy-4'-biphenyl)-2-(4-hydroxyphenyl)butane (TPB) with 1,7-dibromoheptane (TPB-7(c)] are described. These oligomers were synthesized by the phase transfer catalysed polyetherification of TPB with 1,7-dibromoheptane under high dilution conditions and separated by column chromatography. Their cyclic structure was confirmed by 200 MHz ¹H NMR spectroscopy. The mesomorphic behaviour of TPB-7(c) was characterized by differential scanning calorimetry and polarized optical microscopy. The cyclic dimer is only crystalline, while the cyclic trimer, tetramer and pentamer exhibit an enantiotropic nematic mesophase. The high molecular weight linear homologue TPB-7(1) exhibits a nematic mesophase which has an isotropization transition temperature located in the very close proximity of its glass transition temperature. Therefore, this nematic phase is kinetically controlled. Due to the higher rigidity of cyclics versus linear structures the cyclic trimer, tetramer and pentamer exhibit higher isotropization transition temperatures than their linear homologue. Subsequently, the kinetically controlled nematic mesophase of the linear homologue is transformed into a thermodynamically controlled phase via cyclization.     

Determination of the changes of the basic structures of silica species in dependence on the concentration of sodium chloride by FAB-MS

The chemical species of silica in NaCl solutions of different concentrations were identified by FAB-MS (fast atom bombardment mass spectrometry). The basic structures of silica species, such as cyclic pentamer (Si5 (OH)9O6-), linear pentamer (Sis(OH)11O5-), cyclic hexamer (Si6(OH)9O8-, Si6(OH)11O7-) and linear hexamer (Si6(OH)14 O6-), were identified, in addition to dimer (Si2(OH)5O2-), trimer (Si3(OH)7O3-) and cyclic tetramer (Si4(OH)7O5-). The patterns of changes of the peak intensities of the silicate complexes relative to the dimer with increasing NaCl concentration were classified into two types: that represented by linear silicate complexes and the other by cyclic silicate complexes. The differences in the type of chemical species and their changes according to the NaCl concentration reflect the number of bonds necessary for polymerization and hydrolysis of the silica complexes. The differences between the linear and the cyclic silicate type have some implications on the dissolution mechanism of silicate complexes, the hydration of the molecules and the equilibrium between solubility, hydrolysis, polymerization and the salting-out effect in NaCl solution.     

聚(对苯二甲酸-1,3-丙二酯)环状低聚物的合成、表征和开环聚合反应

探索了由对苯二甲酰氯和1,3-丙二醇在“假高稀”条件下合成聚(对苯二甲酸-1,3-丙二酯)(PTT)环状低聚物的可行性.通过柱色谱分离了环状低聚物和线形低聚物;用核磁共振、质谱和元素分析表征了产物的化学结构;用GPC和HPLC研究了不同大小环的分布,发现在本文实验条件下合成的PTT环状低聚物主要由二、三、四、五和七聚体构成,其中环状三聚体含量最多,没有发现环状六聚体的存在.PTT环状低聚物的熔程为92.3～222.6℃,熔融后是无色、透明的低粘度液体.于250℃将PTT环状低聚物分别在辛酸亚锡、1-乙基-3-氯四丁基锡氧烷、钛酸四丁酯和三氧化二锑催化下进行开环聚合反应,制备了特性粘数为0.18～0.49dL/g的聚合物.     

Infrared absorption of methanol clusters (CH3OH)n with n = 2-6 recorded with a time-of-flight mass spectrometer using infrared depletion and vacuum-ultraviolet ionization

We investigated IR spectra in the CH- and OH-stretching regions of size-selected methanol clusters, (CH(3)OH)(n) with n = 2-6, in a pulsed supersonic jet by using the IR-VUV (vacuum-ultraviolet) ionization technique. VUV emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer. The tunable IR laser emission served as a source of predissociation or excitation before ionization. The variations of intensity of protonated methanol cluster ions (CH(3)OH)(n)H(+) and CH(3)OH(+) and (CH(3)OH)(2)(+) were monitored as the IR laser light was tuned across the range 2650-3750 cm(-1). Careful processing of these action spectra based on photoionization efficiencies and the production and loss of each cluster due to photodissociation yielded IR spectra of the size-selected clusters. Spectra of methanol clusters in the OH region have been extensively investigated; our results are consistent with previous reports, except that the band near 3675 cm(-1) is identified as being associated with the proton acceptor of (CH(3)OH)(2). Spectra in the CH region are new. In the region 2800-3050 cm(-1), bands near 2845, 2956, and 3007 cm(-1) for CH(3)OH split into 2823, 2849, 2934, 2955, 2984, and 3006 cm(-1) for (CH(3)OH)(2) that correspond to proton donor and proton acceptor, indicating that the methanol dimer has a preferred open-chain structure. In contrast, for (CH(3)OH)(3), the splitting diminishes and the bands near 2837, 2954, and 2987 cm(-1) become narrower, indicating a preferred cyclic structure. Anharmonic vibrational wavenumbers predicted for the methanol open-chain dimer and the cyclic trimer with the B3LYP∕VPT2∕ANO1 level of theory are consistent with experimental results. For the tetramer and pentamer, the spectral pattern similar to that of the trimer but with greater widths was observed, indicating that the most stable structures are also cyclic.     

A twelve-connected porous framework built from rare linear cadmium tricarboxylate pentamer

A twelve-connected 3D metal-organic framework built from a rare linear Cd(5)(COOR)(12) pentamer with selective CO(2) uptake, has been prepared and characterized, together with a 2D framework based on a shorter linear Cd(3)(COOR)(6) trimer.     

Interactions of silicate ions with zinc(II) and aluminum(III) in alkaline aqueous solution

We present (29)Si, (27)Al, and (67)Zn NMR evidence to show that silicate ions in alkaline solution form complexes with zinc(II) (present as zincate, Zn(OH)(3)(-) or Zn(OH)(4)(2-)) and, concomitantly, with aluminate (Al(OH)(4)(-)). Zincate reacts with monomeric silicate at pH 14-15 to form [(HO)O(2)Si-O-Zn(OH)(3)](4-) and with dimeric silicate to produce [HO-SiO(2)-O-SiO(2)-O-Zn(OH)(3)](6-). The exchange of Si between these free and Zn-bound sites is immeasurably fast on the (29)Si NMR time scale. The cyclic silicate trimer reacts relatively slowly and incompletely with zincate to form [(HO)(3)Zn{(SiO(3))(3)}](7-). The concentration of the cyclic trimer becomes further depleted because zincate scavenges the silicate monomer and dimer, with which the cyclic trimer is in equilibrium on the time scale of sample preparation. Identification of these zincate-silicate complexes is supported by quantum chemical theoretical calculations. Aluminate and zincate, when present together, compete roughly equally for a deficiency of silicate to form [(HO)(3)ZnOSiO(2)OH](4-) and [(HO)(3)AlOSiO(2)OH](3-) which exchange (29)Si at a fast but measurable rate.     

Electric field effects on water clusters (n = 3-5): systematic ab initio study of structures, energetics, and transition states

The structures, energetics, and transition states of water clusters (trimer to pentamer, n = 3-5) are investigated as a function of electric field by using ab initio calculations. With an increasing strength of the field, the most stable cyclic structures of trimer, tetramer, and pentamer open up to align their dipole moments along the direction of the field. For the lower strength (below 0.3 V/angstroms) of the electric field, the dipole moment of each water monomer is along the same direction with the field, while it retains the cyclic structure. For the higher strength of the field, to have a higher dipole moment for the cluster along the field direction, each cyclic structure opens up to form a linear chain or "water wire." We have investigated the transition state structures between the cyclic and linear forms for the field strengths of 0.3-0.4 V/angstroms where both cyclic and linear forms are energetically comparable.     

Organic spin clusters: macrocyclic-macrocyclic polyarylmethyl polyradicals with very high spin S = 5-13

Synthesis and magnetic studies of a new class of organic spin clusters, possessing alternating connectivity of unequal spins, are described. Polyarylmethyl polyether precursors to the spin clusters, with linear and branched connectivity between calix[4]arene-based macrocycles, are prepared via modular, multistep syntheses. Their molecular connectivity and stereoisomerism are analyzed using NMR spectroscopy. The absolute masses (4-10 kDa) are determined by FABMS and GPC/MALS. Small angle neutron scattering (SANS) provides the radii of gyration of 1.2-1.8 nm. The corresponding polyradicals with 15, 22, and 36 triarylmethyls, which are prepared and studied as solutions in tetrahydrofuran-d(8), may be described as S' = 7/2, 1/2, 7/2 spin trimer (average S = 5-6), S' = 7/2, 1/2, 6/2, 1/2, 7/2 spin pentamer (average S = 7-9), and spin nonamer (average S = 11-13), respectively, as determined by SQUID magnetometry and numerical fits to linear combinations of the Brillouin functions. For spin trimer and pentamer, the quantitative magnetization data are fit to new percolation models, based upon random distributions of chemical defects and ferromagnetic vs antiferromagnetic couplings. The value of S = 13 is the highest for an organic molecule.     

Special odd-even effect of degree of oligomerization on properties of cyclic oligoesters

We demonstrate here seven pure cyclic samples,which belongs to two series of oligoesters,cyclic oligo(trimethylene terephthalate)s(COTTs) and cyclic oligo(butylene terephthalate)s(COBTs),showing odd-even effect of degree of oligomerization(repeating units number) on properties.The pentamer of COTT and trimer of COBT show much lower melting temperature,and the trimer of COTT and trimer of COBT show significant lower refractive index,which can be ascribed to the low packing density of cyclic oligoesters with odd number of degree of oligomerization.Our results reveal the discrete property change as a function of cyclic size of oligomers,which can be used to design materials with special properties.     

Structure of complexes formed by dissolution of palladium diacetate in methanol and chloroform. In situ NMR study

The behavior of palladium diacetate cyclic trimer [Pd(OAc)(2)](3) (1) upon its dissolution in methanol and wet chloroform was studied by (1)H and (13)C NMR including 2D-HSQC and 2D-DOSY techniques. Upon dissolution, trimer 1 reacts with methanol and is completely transformed first into the methoxo complex Pd(3)(μ-OMe)(OAc)(5) (2), which already at -18 °C undergoes a slow exchange of second bridging acetate ligand between the same palladium atoms to form the symmetric dimethoxo complex Pd(3)(μ-OMe)(2)(OAc)(4), the maximum relative concentration of which reaches 20-30 mol % of initial loading trimer 1. Along with the dimethoxo complex, both soluble and insoluble polynuclear palladium clusters are gradually formed at -18 °C, and their total amount reaches up to 60% of the starting Pd(2+) loading. The increase of temperature to 27 °C results in the reduction of palladium(II) to Pd metal by methanol, which is oxidized and transformed into formaldehyde hemiacetal and methyl formate. Upon dissolution in wet chloroform, trimer 1 is reversibly hydrolyzed to the hydroxo complex Pd(3)(μ-OH)(OAc)(5) (10) in ratio 1/10 ≈ 3/1. The temperature decrease and addition of acetic acid shift the equilibrium in this system toward trimer 1, and addition of water shifts it in the opposite direction. Addition of methanol to the equilibrium mixture of 1 and 10 results in the fast exchange of bridging acetate in trimer 1 by the μ-OMe group. Substitution of the μ-OH ligand by μ-OMe in 10 occurs in parallel but more slowly. Complex 2 formed in both cases is more stable in chloroform than in methanol.     

Highly conjugated multiporphyrins: synthesis, spectroscopic and electrochemical properties

A series of meso-to-meso ethynyl-bridged multiporphyrin arrays have been synthesized using Sonogoshira palladium-catalyzed cross-coupling reactions involving the appropriate ethynylporphyrin and iodoporphyrin precursors. The absorption spectra of these multiporphyrins show splitting of the Soret bands and significant red shifts of the Q bands as compared to the combination of the corresponding components. These conjugated multiporphyrins also show red shifts in their emission spectra as the pi-conjugation is expanded. In the electrochemical measurements, the porphyrins dimer 7 shows two 1 - e- oxidations at E(1/2) = +0.63 and +0.76 V for the first electron abstraction from the two porphyrin rings, indicating electronic communication between the two porphyrin units. The porphyrin trimer 4 exhibits the first and second 1 - e- oxidations at E(1/2) = +0.68 and +0.77 V, respectively, which correspond to the two outer porphyrins. The cyclic voltammogram of pentamer 5 shows two overlapping 1 - e- couples at E(1/2) = +0.56 and +0.66 V, and one 2 - e- couple at E(1/2) = +0.86 V, for the four outer porphyrin units. These results demonstrate that in the porphyrin trimer and pentamer the individual peripheral porphyrin units are electrochemically coupled via a central porphyrin core. The UV-Vis-NIR spectra of the oxidized species of these multiporphyrins exhibit a broad intervalence charge transfer (IVCT) band in the region from 1200 to 3000 nm. The present work shows that a central porphyrin unit appended with ethynyl bridges affords strong electronic interactions between the peripheral porphyrin rings over a distance of about 15 A.     

A New Helicopodand: Molecular Recognition of Dicarboxylic Acids with High Diastereoselectivity

The helicopodand (PM)- 2 is prepared following the photocyclodehydrogenation route to helicenes (Scheme). At the ends of a [7]helicene backbone, this acyclic receptor (‘podand’) possesses a H-bonding recognition site shaped by two convergent N-(pyridin-2-yl)carboxamide (CONH(py)) units. In the crystal of diethyl [7]helicene-2,17-dicarboxylate ((PM)- 3 ), a direct synthetic precursor of 2 , molecules of the same chirality form stacks, and two stacks of opposite chirality are interlocked in a pair having average face-to-face aromatic contacts of 3.82 Å between benzene rings of different enantiomers (Fig. 2). In contrast, two conformations are observed in the crystal structure of 2 , one with both CONH(py) residues pointing with their H-bonding centers NH/N away from the binding site (‘out-out’) and a second (‘in-out’) with one of the two CONH(py) residues pointing towards the binding site (‘in’; Fig. 4). While no H-bonding network propagates throughout the crystal, enantiomers of 2 in the different conformations ‘out-out’ and ‘in-out’ form H-bonded pairs that are further stabilized by a H-bond to one molecule of CHCl₃. In the productive ‘in-in’ conformation, 2 forms stable 1:1 complexes with α,ω-dicarboxylic acids in CHCl₃, and a diastereoselectivity in complexation of Δ(ΔG°) = 1.4 kcal mol^?1 is measured for two substrates differing only in the (E)/(Z)-configuration at their double bond (see Table 2). A comprehensive force-field molecular-modeling study suggests that only the (E)-derivative possesses the correct geometry for a ditopic four-fold H-bonding interaction between its two COOH residues and the two CONH(py) groups in 2 (Fig. 5). With N,N′-bis [(benzyloxy)carbonyl]-L -cystine, the formation of diastereoisomeric complexes with (PM)- 2 is observed (Fig. 7).     

Global search for minimum energy (H2O)n clusters, n = 3-5

The Gaussian-3 (G3) model chemistry method has been used to calculate the relative deltaG(o) values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3-5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20,736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.     

Oligonucleosides with a Nucleobase‐Including Backbone. Part 11

A linear and a convergent synthesis of uridine‐derived backbone‐base‐dedifferentiated (backbone including) oligonucleotide analogues were compared. The Sonogashira cross‐coupling of the alkyne 1 and the iodide 2 gave the dimer 4 that was C‐desilylated and again coupled with 2 to give the trimer 6 (Scheme 1). Repeating this linear sequence led to the pentamer 10 . Coupling yields were satisfactory up to formation of the trimer 6 , but decreased for the coupling to higher oligomers. Similarly, coupling of the alkynes 5, 7 , and 9 with the iodouridine 3 gave, in decreasing yields, the trimer 12 , tetramer 13 , and pentamer 14 , respectively. The dimeric iodouracil 20 was synthesized by coupling the alkyne 17 with the iodide 16 to the dimer 18 , followed by iodination at C(6/I) to 19 and O‐silylation (Scheme 2). The iodinated dimer 23 was prepared by iodinating and O‐silylating the known dimer 21 . Coupling of 20 and 23 with the dimer 5 , trimer 7 , and tetramer 9 gave the tetramers 8 and 13 , the pentamers 10 and 14 , and the hexamer 15 , respectively (Scheme 3). The oligomers up to the pentamer 14 were deprotected to provide the trimer 24 , tetramer 25 , and pentamer 26 (Scheme 4). There was no evidence for the heteropairing of the pentamer 26 and rA₇ , nor for the pairing of rU₅ and rA₇, while a UV melting experiment showed the beginning of a sigmoid curve for the interaction of rU₇ with rA₇. Therefore, the pentamer 26 does not pair more strongly with rA₇ than rU₅.     

A unique cyanide-bridged three-dimensional (3-D) copper(II)-copper(I) mixed-valence polymer containing 1-D water tapes with cyclic pentamer units

A unique cyano-bridged copper(II)-copper(I) mixed-valence polymer, {[Cu(3)(CN)(4)(H(2)O)(3)](H(2)O)(2)}(n) (1), has been prepared and structurally determined by X-ray diffraction. The cyanide anions with (mu(2),eta(2)) and (mu(3),eta(2)) bridging modes connect the copper centers into a complicated zeolite-like 3-D network. Of further interest, coordinated and lattice water molecules in this structure form 1-D hydrogen-bonded water tapes consisting of linked cyclic pentamer clusters.     

Prediction of accurate anharmonic experimental vibrational frequencies for water clusters, (H2O)n, n=2-5

Accurate anharmonic experimental vibrational frequencies for water clusters consisting of 2-5 water molecules have been predicted on the basis of comparing different methods with MP2/aug-cc-pVTZ calculated and experimental anharmonic frequencies. The combination of using HF/6-31G* scaled frequencies for intramolecular modes and anharmonic frequencies for intermolecular modes gives excellent agreement with experiment for the water dimer and trimer and are as good as the expensive anharmonic MP2 calculations. The water trimer, the cyclic Ci and S4 tetramers, and the cyclic pentamer all have unique peaks in the infrared spectrum between 500 and 800 cm-1 and between 3400 and 3700 cm-1. Under the right experimental conditions these different clusters can be uniquely identified using high-resolution IR spectroscopy.     

Cyclic and ladder hydrogen bonded cyanamide oligomers: a density functional theory and many-body analysis approach

This work reports hydrogen bonding interaction in cyclic and ladder oligomers using density functional theory method. Many-body analysis technique has been used to study the nature of interactions between different molecules and their contribution to the binding energy of a respective hydrogen bonded oligomers. Hydrogen bonds in cyclic trimer to pentamer are stronger than those in corresponding ladder structures. Cyanamide monomer shows the lowest energy at B3LYP/aug-cc-pvdz level among different methods used here with the same basis set. The geometrical parameters for cyanamide monomer obtained at B3LYP/aug-cc-pvdz level are in excellent agreement with the experimental determinations. Cyclic structures are more stable than the ladder. In cyclic oligomers not only total two-body energies, but higher body energies also contribute significantly to the binding energy of a respective complex whereas in ladder, only total two-body energies contribute significantly and higher-body energies are almost negligible for cyanamide trimer to pentamer.     

Proton transfer of NH3-HCl catalyzed by only one molecule

The proton transfer in NH(3)-HCl by only one molecule of catalyst was studied by using the MP2 method with the large 6-311++G(2d,2p) basis set. The 18 structures are obtained for the smallest units, NH(3)-HCl-A trimers, for which the proton transfer maybe occurred. The final results show that the proton transfers have occurred in the 15 cyclic shape structures for A = H(2)SO(4), H(2)SO(3), HCOOH (a), HF, H(2)O(2), HNO(3), HNO(2) (a), CH(3)OH, HCl, HNC, H(2)O, HNO(2) (b), NH(3), HCOOH (b), and HCHO, and not occurred in another 3 trimer structures for A = HCN, H(2)S, and PH(3). These results show that the proton transfer occurs from HCl to NH(3) when catalyst molecule A (acidic, neutral, or basic) not only as a proton donor strongly donates the proton to the Cl atom but as an acceptor strongly accepts the proton from the NH(3) molecule in the cyclic H-bond structure. In this work, a proton circumfluence model is proposed to explain the mechanism of the proton transfer. We find that, for the trimer, when the sum of two hydrogen bond lengths (R = R(1) + R(2)) is shorter than 5.0 A, molecule A has the ability to catalyze the proton transfer. In addition, we also find that the interaction energy E(int) between NH(3)-HCl and A is nearly related to the extent (R(H1)(-)(Cl)) of proton transfer, that is, the interaction energy E(int) increases with the proton transfer.     

Interaction of first row transition metals with α1-3, α1-6 mannotriose and conserved trimannosyl core oligosaccharides: A comparative electrospray ionization study of doubly and singly charged complexes

Electrospray ionization and tandem mass spectrometry were used in the analysis of metalcoordinated oligosaccharides. Four transition metal ions, Cu²⁺, Mn²⁺, Co²⁺, and Zn²⁺, and the alkaline earth metal ion Ca²⁺, were each coordinated to the trimer α1–3, α1–6 mannotriose and the pentamer conserved trimannosyl core (mannotriosyl-chitobiose). Instrumental and concentration ratio optimization studies were carried out to determine the best conditions for producing the [M + Met]²⁺, [M + MetCl]⁺, and [M + Met ? H]⁺ ions (Met = metal dication). These precursors were then subjected to tandem mass spectrometry (MS/MS) analysis and compared. Both the ionic radii and efficacy of ligand coordination were observed as important criteria for producing the precursor ions. Tandem mass spectra for the Cu²⁺- and Zn²⁺-coordinated species did not produce significant structural information about either the trimer or the pentamer. Although tandem mass spectra for the Ca²⁺-, Co²⁺-, and Mn²⁺-coordinated trimer were very similar, those of the pentamer were not. MS/MS of the Co²⁺-coordinated pentamer was the most unique and exhibited very different dissociation pathways.