Stereoselective self-sorting in the self-assembly of a Phe-Phe extended guanidiniocarbonyl pyrrole carboxylate zwitterion: formation of two diastereomeric dimers with significantly different stabilities

The 'dipeptide extended' guanidiniocarbonyl pyrrole carboxylate zwitterion GCP-Phe-Phe 1 forms stable dimers in DMSO. However, dimerization is highly stereoselective. Only homochiral dimers are formed and the (L,L)·(L,L) dimer (K(dim) > 10(5) M(-1)) is significantly more stable by a factor of 10(3) than the diastereomeric (D,L)·(D,L) dimer (K(dim) = 120 M(-1)).     

FTIR spectra of HSCH2CH2SH,CH3SCH2SH,and CH3SSCH3 in argon and nitrogen matrices

Matrix-isolated IR spectra of 1,2-ethanedithiol, (methylthio)methanethiol, and dimethyldisulfide were recorded from 400 to 4000 cm⁻¹ in argon and nitrogen matrices at 12 K. The appearances of new bands around the vibrations of the monomers provide evidence for the presence of dimer and multimers of 1,2-ethanedithiol and (methythio)methanethiol in argon and nitrogen matrices. The co-existence of two different dimers of (methylthio)methanethiol in nitrogen matrices is considered on the basis of the experimental data. The spectroscopic data confirm the presence of one gauche and one trans conformer for 1,2-ethanedithiol and at least three conformers for (methylthio)methanethiol, but only one gauche form for dimethyl disulfide in the matrices.     

Colorful Friedel-Crafts chemistry of meso-tetraarylporphyrins. An unexpected route to porphyrinic spiro dimers

Under Friedel-Crafts conditions, meso-tetraarylporphyrins give porphyrin spiro dimers in good yield. This reaction involves acylation, acid-catalyzed cyclization, and dimerization. A stable dimer possessing three additional six-membered rings could be isolated and its structure determined. By modifying the substrate and reagents, intermediates could be isolated and characterized. The reactivity of the substrates, the side-reactions, and the concentration requirements to form the dimers, all explain why this reaction remained apparently unexplored in the widely used meso-tetraarylporphyrin series. [reaction: see text]     

Excess molar volumes of formic acid + water acetic acid + water and propionic acid + water systems at 288.15, 298.15 and 308.15 K

Densities and excess molar volumes were determined in the formic acid + water, acetic acid + water and propionic acid + water systems at 288.15, 298.15 and 308.15 K. The results are satisfactorily described using the ideal association model of the type A + B + A₂ for the system with formic acid. The Mecke—Kempter model is adequate for the acetic acid + water and propionic acid + water systems. In both models the formation of open dimers and open higher associates is postulated for the self-association of carboxylic acids in water.     

Dimerization of formic acid--an example of a "noncovalent" reaction mechanism

The pulse deposition technique allows selectively the isolation of monomeric or dimeric formic acid in argon matrices at 7 K. Warming of matrices containing the monomer M from 7 K to 40 K results in the decrease of M and formation of a dimer B. This dimer is also labile, and further warming finally produces a second dimer A. By comparison with density functional theory (DFT) calculations and gas phase IR spectra taken from the literature, the latter dimer A was identified as the C2h-symmetrical cyclic dimer. The unstable dimer B was identified as the acyclic Cs-symmetrical dimer. An activation energy of 2.3 kcal mol(-1) was calculated for the B --> A rearrangement at the B3LYP/ 6-311 ++ G(d,p) level of theory, which is in qualitative agreement with the experimental finding of a slow thermal reaction under the conditions of matrix isolation.     

A DFT study on the dimerization of C62, H2-C62, and F2-C62

On the basis of calculations using the density functional theory, we show that C(62), a recently synthesized nonclassical fullerene, will presumably undergo dimerization with various isomers at elevated temperatures. This is shown by calculating the dimerization energy and the activation barrier of the dimerization. Eight possible isomers of the dimer were identified, all of which are more stable than the two isolated monomers. The relative stability of various isomers depends upon the kind of C=C bonds within the four-membered carbon ring involved in the dimerization. In addition, similar calculations were performed for the monomers and dimers of H(2)-C(62) and F(2)-C(62). Six isomers were identified for each of the dimers. Although less pronounced than the case of the C(62) dimer, all isomers of the H(2)-C(62) dimer are appreciably more stable than the individual monomers. Although a large steric repulsion due to F atoms significantly reduces the stability of F(2)-C(62) dimer, its two isomers are still more stable than separate monomers.     

Preferential Solvation of Acetic Acid in Binary Mixtures of Carbon Tetrachloride–Cyclohexane and Carbon Tetrachloride–1,2-Dichloroethane

The partition of acetic acid between aqueous solutions and various binary mixtures of carbon tetrachloride + cyclohexane and carbon tetrachloride + 1,2-dichloroethane were carried out at 30.0 °C. The nonlinear dependence of both the monomer partition coefficient and the dimerization constant on the mole fraction composition has been rationalized in terms of preferential solvation of the various solvation sites of the involved species. Two and four polar sites were identified for the monomer and dimer forms, respectively. The solvation preference is controlled by the relative polarities of the binary solvent components, being, in general, higher for the monomer sites compared to the dimer ones. The dimer is almost equally stable in various carbon tetrachloride + 1,2-dichloroethane mixtures, and the variation of dimerization constants with changing binary composition arises mainly from the monomer solvation stabilization.     

The ν(OH/OD) band shape of strong hydrogen bonded dimers of phosphinic acids. Phenomenology and formation models

The infrared spectra of phosphinic acid R₂POOH dimers (R=CH₃, CH₂Cl, C₆H₅) have been studied in CCl₄ and CH₂Cl₂ solutions (T=300 K). The infrared spectra of deuterated R₂POOD dimers (R=CH₃, CH₂Cl) were also studied in the gas phase (T=400–550 K) and solid state (T=100–300 K). They are compared with previously studied spectra of the light (non-deuterated) dimers in the gas phase, in the solid state and in low-temperature argon matrices (T=12–30 K) in the 4000–400 cm⁻¹ spectral region. It is found that the strong and broad ν(OH) dimer bands have similar shapes, nearly equal values of bandwidth and low-frequency shift, and possess the Hadzi ABC structure irrespective of the type of acid, significant differences of dimerization enthalpies, influence of solvent, the type of H-bonded complexes (cyclic dimers in the gas phase, in solutions, and in inert matrices, and infinite chains in the solid state), and temperature in the range 12–600 K. Isotopic ratio of the first moments of light and deuterated acid bands has been measured. Analysis of the ν(OH/OD) band of hydrogen bonded dimers of phosphinic acids shows that the interaction between the two intermolecular bonds O–HOP in a cyclic complex plays virtually no role in the mechanism of the ν(OH/OD) band formation; the shape of ν(OH/OD) band is controlled mainly by the POOH(D)O fragment; and the band shape of strong hydrogen bonded complexes is formed by a number of vibrational transitions from the ground state to different combination levels in the region 3500–1500 cm⁻¹.     

Adsorption of acetic acid on ice: experiments and molecular dynamics simulations

Adsorption study of acetic acid on ice surfaces was performed by combining experimental and theoretical approaches. The experiments were conducted between 193 and 223 K using a coated wall flow tube coupled to a mass spectrometric detection. Under our experimental conditions, acetic acid was mainly dimerized in the gas phase. The surface coverage increases with decreasing temperature and with increasing concentrations of acetic acid dimers. The obtained experimental surface coverages were fitted according to the BET theory in order to determine the enthalpy of adsorption deltaH(ads) and the mololayer capacity N(M(dimers)) of the acetic acid dimers on ice: deltaH(ads) = (-33.5 +/- 4.2) kJ mol(-1), N(M(dimers)) = (l1.27 +/- 0.25) x 10(14) dimers cm(-2). The adsorption characteristics of acetic acid on an ideal ice I(n)(0001) surface were also studied by means of classical molecular dynamics simulations in the same temperature range. The monolayer capacity, the configurations of the molecules in their adsorption sites, and the corresponding adsorption energies have been determined for both acetic acid monomers and dimers, and compared to the corresponding data obtained from the experiments. In addition, the theoretical results show that the interaction with the ice surface could be strong enough to break the acetic acid dimers that exist in the gas phase and leads to the stabilization of acetic acid monomers on ice.     

Enol-enamine tautomerism in crystals of 1,3-bis(pyridin-2-yl) propan-2-one: a combined crystallographic and quantum-chemical investigation of the effect of packing on tautomerization processes

The enolpyridine, OH-ketoenamime, NH equilibrium in crystals of 1,3-bis(pyridin-2-yl)propan-2-one was studied using temperature-dependent single-crystal X-ray diffraction. The relative population of the different tautomers was found to be sensitive to the temperature in the range of 100-300 K, illustrating the small thermodynamic difference between these two tautomers. This energy resemblance is partially attributed to the molecular packing in the crystal, where the molecules are arranged in the form of dimers. Ab initio electronic energy calculations (HF/6-31G** and MP2/6-31G**) reveal the effect of dimerization in the crystal on the electronic energy levels. Several tautomeric states were identified in the dimer of 1,3-bis(pyridin-2-yl)propan-2-one. A model is proposed in which four of these dimer states are populated in the crystal at ambient temperatures. The crystallographic data were treated according to this four-state dimer model, suggesting that the free energy of the OH-NH dimers is higher than that of the OH-OH dimers by 120 +/- 10 cal mol(-1) and that the NH-NH dimers are yet higher in free energy by 50 +/- 10 cal mol(-1).     

Vibrational spectra,normal coordinate analyses,and molecular configurations of crystalline propionic acid

Temperature dependence of the IR spectra of crystalline propionic acid were examined in the temperature range 242–50 K. The intensities of most absorption bands increased on lowering the temperature, but some bands diminished until they disappeared at temperatures lower than about 120 K. Normal coordinate analyses indicate that the former bands are due to the stable cis dimer and the latter due to the less stable trans dimer which would be produced from the cis dimer by simultaneous proton transfer along two hydrogen bonds.     

Pyridine Dimers and Their Low-Temperature Isomerization: A High-Resolution Matrix-Isolation Spectroscopy Study

The bonding between two neutral aromatic compounds, especially small ones, has been controversially debated in the last decades, and terms like “π-stacking” had to be revised. Surprisingly, despite of many experimental and computational work, there is still no clear consensus about the structure of and the bonding in the pyridine dimer. In this work, for different isomeric forms of the pyridine dimer, the structures and bonding were elucidated by combining high-resolution matrix-isolation spectroscopic results with quantum-chemical calculations. High-resolution IR spectra of Ne matrices at 4 K containing pyridine were recorded for different concentrations and upon annealing to 10 and 12 K, relying on three isotopologues of pyridine. The spectra show the presence of hydrogen-bonded, T-shaped, and stacked forms of weakly-bound pyridine dimers. Among these, the hydrogen-bonded isomer is identified as the lowest-energy form. The results provide for the first time conclusive information about the interaction between two pyridine dimers.     

Rotational isomers of small molecules in noble-gas solids: From monomers to hydrogen-bonded complexes

Molecular conformation, quantum tunneling, and hydrogen bonding play important roles in various photochemical processes. We have studied a number of small molecules possessing rotational isomerism (HONO, formic acid, acetic acid, etc.) isolated in noble-gas solid matrices. Selective vibrational excitation efficiently promotes the conformational change in the excited molecule, which allows preparation of higher-energy conformers. Stability of the higher-energy conformers is often limited by quantum tunneling of hydrogen as observed for some carboxylic acids (formic, acetic, etc.). The tunneling mechanism is supported by the strong H/D isotope effect and characteristic temperature dependence with a clear low-temperature limit. The reaction barrier height is an important factor in a tunneling process; however, other factors also play an essential role. The energy mismatch between the initial state of the higher-energy conformer and accepting state of the ground-state conformer is probably important. Hydrogen bonding can change tunneling decay rate of unstable conformers. The trans–cis formic acid dimer was prepared by vibrational excitation of the trans–trans form in neon and argon matrices. Tunneling decay of cis formic acid is substantially slower in the dimeric form compared to monomer, especially in solid neon. This stabilization effect is explained by a complexation-induced increase of reaction barrier, which is confirmed computationally. The complex between cis formic acid and water was prepared in an argon matrix and found to be stable at low-temperatures. These results show that intrinsically unstable conformational structures can be thermodynamically stabilized in asymmetrical hydrogen-bonded network. This effect occurs when the energy difference between conformers is smaller than the hydrogen bond interaction energy, which allows chemistry of unstable conformers to be studied.     

Chemically and Electrochemically Triggered Assembly of Viologen Radicals: Towards Multiaddressable Molecular Switches

We have established that bipyridinium radicals can be reversibly π‐dimerized under the combined effects of chemical (proton transfer) and electrochemical (electron transfer) stimuli. Our investigations also led to the discovery that a bis‐pyridinyl appended calixarene intermediate is involved in a fully reversible redox‐triggered σ‐dimerization process. The structure of the most stable intramolecular σ‐dimer was provided by computational chemistry and its complete conversion into a noncovalent π‐dimer could be triggered chemically by addition of protons, leading to the formation of protonated cation radicals. Theoretical data collected with the N‐methylated and N‐protonated π‐dimers also support the existence of multivariant orientations in π‐bonded dimers of viologen cation‐radicals.     

The phenoxyl radical-water complex--a matrix isolation and computational study

The phenoxyl radical 1 was generated in high yields by flash vacuum pyrolysis of allyl phenyl ether 2 with subsequent trapping of the products in argon at 3 K. In water-doped argon matrices, an OH···O complex between 1 and water is formed that could be characterized by IR spectroscopy. Several isotopomers of the complex were generated, and the IR spectra compared to results of density functional theory calculations. Other dimers between 1 and water were not found under these conditions. QM/MM calculations in simulated argon matrices reveal that an OH···π complex is unstable even at a time scale of picoseconds. This finding has implications on the related interaction between the tyrosyl radical and the water in biological systems.     

大气中一元酸催化亚硫酸分解反应的从头算及动力学研究

采用从头算的理论计算方法,在CCSD（T）/aug-cc-pVDZ//MP2/aug-cc-pVDZ水平下,对甲酸、乙酸、丙酸和硝酸催化亚硫酸分解成二氧化硫和水的微观反应机理进行了理论研究.结果表明,这4种一元酸均可使亚硫酸分解反应能垒显著降低,降低幅度由大到小的顺序为丙酸 > 乙酸 > 甲酸 > 硝酸.其中,丙酸甚至使反应能垒从裸反应时的99.84 kJ/mol降至27.24 kJ/mol.在此基础上,计算了200~320 K温度范围内4种一元酸催化亚硫酸分解反应的速率常数,并结合它们在大气中的实际浓度计算了有效速率常数.结果表明,在实际大气环境中,乙酸对亚硫酸分解反应的催化效果最为显著.当乙酸存在时,亚硫酸在室温下的大气寿命仅为0.02 s.     

Experimental dipole moments for nonisolatable acetic acid structures in a nonpolar medium. A combined spectroscopic, dielectric, and DFT study for self-association in solution

Acetic acid can exist in many possible structural forms depending on its surrounding medium. A recently developed inverse problem methodology (J. Phys. Chem. B 2007, 111, 13064-13074) was utilized in order to elucidate acetic acid structures in a dilute nonpolar medium. In this regard, simultaneous and stopped-flow measurements of the bulk solution densities, refractive indices, relative permittivities, and IR spectra of acetic acid in toluene were performed at several different concentrations in a semibatch closed-loop experimental setup at 298.15 K and 0.1013 MPa. This combined IR spectroscopic and dielectric, density, and refractive index analysis was employed in order to distinguish acetic acid structures and to further determine the dipole moments of the monomer, cyclic dimer, and "lumped-sum" open dimers. The infrared spectra were first analyzed to provide qualitative understanding as well as quantitative estimates for each acetic acid species. Subsequently, the dipole moments of these species were calculated using a direct approach which was primarily based on response surface models. The present method allows the determination of individual dipole moments not only for the monomer but also for the cyclic dimer and the open dimer. The results obtained from this study experimentally show that the cyclic dimer with centrosymmetric structure has a dipole moment approximately 0 D. The results also suggest that the linear dimers are present as mixtures of linear dimers structures. The existence of the linear dimers mixture was also indicated by the experimental infrared analysis of the OH-stretching region (particularly for measurements in n-hexane as solvent) and comparison of these spectra with DFT predictions. Finally, the present methodology which incorporates simultaneous physicochemical and spectroscopic analysis is undoubtedly useful for physicochemical characterization for other nonisolatable solute species and self-associated structures in solution.     

Adsorption studies of acetic acid dimers on activated charcoal from organic solvents

Acetic acid exists as dimers in organic solvents like benzene, toluene and xylene. Adsorption of dimeric acetic acid on activated charcoal (AC) at various temperatures from benzene, toluene and xylene solutions have been studied. The system obeys Langmuir isotherm, thus signifying a monolayer adsorption of dimers. Corrections on AC-solvent pore volume fillings, molecular cross sectional surface area of acetic acid dimers, the adsorption equilibrium constants, the free energy change and the enthalpy change values are computed at different temperatures for the three solvents. The adsorption process has been found to be physisorption type. The FTIR measurements show that the adsorbed acetic acid dimer seems to retain the cyclic structure against the open chain non-cyclic structure.     

化学镀镍过程中丙酸作用的机理研究

利用循环伏安法和红外漫反射光谱法研究化学镀镍过程中丙酸的作用机理. 不同丙酸浓度下的循环伏安曲线表明,丙酸能同时促进Ni^2＋的还原和H₂PO^-₂的氧化.根据丙酸分别与NaH₂PO₂和NiSO₄共存时镍基体上吸附物的红外漫反射光谱变化,推断丙酸是通过与NaH₂PO₂和Ni^2＋形成表面络合物来促进化学沉积的. 丙酸能与NaH₂PO₂形成分子间氢键,促使P-H键断裂并生成·PHO^-₂中间物,从而提高H₂PO^-₂的氧化速度; 同时,丙酸以其-OCO-官能团与Ni^2＋生成桥式配合物,有利于加速Ni^2＋的沉积. H₂PO^-₂氧化速度的提高有助于磷的沉积,从而增大了化学镀层中的磷含量.     

1H-ANTA二聚体分子间相互作用的密度泛函理论研究

在DFT-B3LYP/6-311＋＋G**水平上求得1H-3-硝基-5-氨基-1,2,4-三唑(1H-ANTA)二聚体势能面上5种优化构型和电子结构. 经基组叠加误差(BSSE)和零点能(ZPE)校正, 求得分子间最大结合能为70.63 kJ/mol. 二聚体的形成使电荷向三唑环转移. 由氢键强弱推断二聚体稳定性的顺序与结合能顺序相一致, 氢键是二聚体的主要作用形式. 对优化构型进行振动分析, 并基于统计热力学求得200.0～800.0 K温度范围内单体形成二聚体的热力学性质变化. 发现在该温度范围所有二聚过程均能自发进行.