Dodecanuclear water cluster in bowl: microwave-assisted synthesis of a heptanuclear cobalt(II) cluster

A heptanuclear double-bowl-like cluster [Co₇(mmp)₆(OH)₆]₂·(ClO₄)₂·12H₂O (1·12H₂O, Hmmp is 2-methoxy-6-methyliminomethyl-phenol) has been synthesized through the microwave-assisted reaction of Co(ClO₄)₂·6H₂O with 2-hydroxy-3-methoxy-benzaldehyde (Hhmb) and methylamine in mixed solvent (acetonitrile : distilled water = 9 : 1) for 29 min. 1·12H₂O was heated until 180 °C and it formed a non-water complex [Co₇(mmp)₆(OH)₆]₂·(ClO₄)₂ (1). The core of 1·12H₂O can be described as a double bowl, while the dodecanuclear water cluster stands on the bowl. Magnetic investigations show that 1·12H₂O and 1 display ferromagnetic interaction between cobalt ions. Moreover, 1 shows single molecular magnet behavior under 2 K. Magnetic studies indicate that hydrogen bond plays a vital role in transferring magnetic exchange effects.     

Zinc oxide: A case study in contemporary computational solid state chemistry

Computational techniques have been applied to study a broad range of chemical and physical properties of zinc oxide. Both interatomic-potential and density functional theory methods are used to investigate structural, thermodynamic, surface, and defect properties. We survey the structures and energies of nano-particulate zinc oxide.     

The gas-phase ozonolysis reaction of methylbutenol: A mechanistic study

The gas-phase ozonolysis reaction of methylbutenol through the Criegee mechanism is investigated. The initial reaction leads to a primary ozonide (POZ) formation with barriers in the range of 10–28 kJ mol⁻¹. The formation of 2-hydroxy-2-methyl-propanal (HMP) and formaldehyde-oxide is more favorable, by 10 kJ mol⁻¹, than the syn-CI and formaldehyde. The unimolecular dissociation of the more stable syn-CI via 1,5-H transfer into an epoxide is more favored than the epoxide and ³O₂ formation. The ester channel led to the formation of the acetone and formic acid favorably from the anti-CI. The hydration of the anti-CI with H₂O and (H₂O)₂ is significantly barrierless with a higher plausibility to the latter, and thus they may lead to the formation of peroxides and ultimately OH radicals, as well as airborne particulate matter. Reaction of anti-CI with water dimers enhances its atmospheric reactivity by a factor of 28 in reference to water monomers.     

Asymmetric acetylenic thioethers in ruthenium cluster chemistry

The compounds [Ru₃(CO)₉(μ,η²-SCCR)(μ₃,η²-CCR^′)] (R=SiMe₃, R^′=SiⁱPr₃ (1); R=SiⁱPr₃, R^′=SiMe₃ (2); R=SiⁱPr₃, R^′=H (3); R=H, R^′=SiⁱPr₃ (4)) have been obtained by cleavage of one S-C bond of the thioethers ⁱPr₃SiCCSCCR (R=H, SiMe₃) in the presence of Ru₃(CO)₁₂. Thermal treatment of [Ru₃(CO)₉(μ,η²-SCCSiⁱPr₃)(μ₃,η²-CCH)] yields to the cluster [Ru₄(CO)₉(μ-CO)₂(μ₄-S)(μ₄-η²-C(H)C)(CCSiⁱPr₃)] (5) which contains a bridging sulfur atom and a polycarbon chain as a consequence of the rupture of the S-C bond and a C-C coupling reaction. All derivatives have been characterized by spectroscopic data. An X-ray diffraction study was carried out on the species [Ru₃(CO)₉(μ,η²-SCCSiⁱPr₃)(μ₃,η²-CCSiMe₃)] and of [Ru₃(CO)₉(μ,η²-SCCSiⁱPr₃)(μ₃,η²-CCH)].     

Monosilicon-substituted cyanoacetylene: a computational study

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.     

单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

Carbonyl coordination chemistry from a new angle: a computational study of alpha-carbon acidity based on electrophile coordination geometry

[reaction: see text] The dependence of acidity on Li+ coordination geometry to alpha-carbon acids is investigated by generating potential energy surfaces of Li+ complexation with acetaldehyde and its respective enolate. The global minimum for the enolate complex shows significant Li+-pi-system coordination to both oxygen and the alpha-carbon. The gas-phase acidity analysis reveals significantly more alpha-carbon coordination, which presumably enhances the lability of the cleaving proton in the transition state of deprotonation.     

JACOB: An enterprise framework for computational chemistry

Here, we present just a collection of beans (JACOB): an integrated batch‐based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user‐specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application‐programming interface provides a set of generic tools for processing large‐scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob . © 2013 Wiley Periodicals, Inc.     

Cuby: An integrative framework for computational chemistry

Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high‐level, object‐oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz . © 2016 Wiley Periodicals, Inc.     

Multicentered bonding and quasi-aromaticity in metal-chalcogenide cluster chemistry

On the basis of the localized molecular orbital (LMO) theory, the bonding schemes for the following types of cluster compounds are briefly reviewed in this paper; the linear [Et₄N][Cl₂FeS₂MoS₂Cu(PPh₃)₂] cluster, triangular trinuclear [M ₃(₃–X)(–Y ₃]⁴⁺ (M = Mo, W;X = O, S;Y = O, S, Se) clusters, triangulated polyhedral clusters: closo-boranes B _n H _n ^2–, octahedral [Co₆(CO)₁₄]^4–, [Ni₂Co₄(CO)₁₄]^2– and [Co₆(₃ –X ₈ ·L ₆ ⁿ⁺ (X = S, Se;L = PPh₃, PEt₃, CO;n = 0,1) as well as quasi-aromatic cluster ligands in cubane-type [Mo₃S₄ ·ML _n ^{(4 +q) +} (M = Mo, W, Fe, Ni, Cu, Sn, Sb;L = Ligand and sandwich-type [Mo₃S₄ ·M · S₄Mo₃]⁸⁺ (M = Mo, Sn, Hg). We put emphasis upon the characteristics of multicentered bonding in these cluster molecules, and, especially, point out existence of a novel species of quasi-aromatic cluster compounds.     

A computational study of interactions between acetic acid and water molecules

Density functional theory calculations were performed for the title reactions to elucidate the difference between the strong cyclic hydrogen bond of (Me-COOH)(2) and the electrolytic dissociation, MeCOOH <==> Me-COO(-) + H(+), as a weak acid. The association of water clusters with acetic acid dimers strengthens the cyclic hydrogen bond. A nucleophilic attack of the carboxylic carbon by a water cluster leads to a first zwitterionic intermediate, MeCOO(-) + H(3)O(+) + (HO)(3)C-Me. The intermediate is unstable and is isomerized to a neutral interacting system, MeCOOH...(HO)(3)C-Me + H(2)O. The ethanetriol, (HO)(3)-CMe is transformed to an acetic acid monomer. The monomer may be dissociated to give a second zwitterionic intermediate with reasonable proton-relay patterns and energy changes. In proton relay reaction channels, H in MeCOOH is not an acidic proton but is always a hydroxy proton.     

An ONIOM and DFT study of water adsorption on rutile TiO2 (110) cluster

Density functional theory (DFT) calculations performed at ONIOM DFT B3LYP/6‐31G**‐MD/UFF level are employed to study molecular and dissociative water adsorption on rutile TiO₂ (110) surface represented by partially relaxed Ti₂₅O₃₇ ONIOM cluster. DFT calculations indicate that dissociative water adsorption is not favorable because of high activation barrier (23.2 kcal/mol). The adsorption energy and vibration frequency of both molecularly and dissociatively adsorbed water molecule on rutile TiO₂ (110) surface compare well with the values reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Supramolecular chemistry in water

Supramolecular chemistry in water is a constantly growing research area because noncovalent interactions in aqueous media are important for obtaining a better understanding and control of the major processes in nature. This Review offers an overview of recent advances in the area of water-soluble synthetic receptors as well as self-assembly and molecular recognition in water, through consideration of the functionalities that are used to increase the water solubility, as well as the supramolecular interactions and approaches used for effective recognition of a guest and self-assembly in water. The special features and applications of supramolecular entities in aqueous media are also described.     

Release of nitric oxide from nitrated fatty acids: Insights from computational chemistry

Nitrated fatty acids (NO₂‐FAs) exhibit a variety of important biological attributes, including a nitric oxide (˙NO) donor and a cell‐signaling molecule. We investigated the mechanisms of fatty‐acid nitration, and the release of ˙NO from NO₂‐FAs. NO₂‐FAs are formed effectively by the addition of ˙NO₂, followed by either hydrogen abstraction or addition of a second NO₂. The latter reaction results in a vicinal nitronitrite ester form of FA, which isomerizes into vicinal nitrohydroxy FA via hydronium ion catalysis. The nitrohydroxy FAs exist in equilibria with NO₂‐FAs. Nitration of conjugated linoleic acid (cLA) was proved to be significantly more efficient than that of LA. In a nonaqueous environment, release of ˙NO from nitrite ester (ONO‐FA) was facilitated by ˙NO₂. Furthermore, the release of ˙NO from NO₂‐cLA is the most favorable in the nitrite ester mechanism. In an aqueous environment, the modified Nef reaction was shown to be feasible. In addition, the release of ˙NO from 10‐ and 12‐NO₂‐LA involves a larger reaction barrier and is more endergonic than those from 9‐ and 13‐NO₂‐LA.     

Coupled‐cluster reaction barriers of : An application of the coupled‐cluster//Kohn–Sham density functional theory model chemistry

In this work, we report a theoretical investigation concerning the use of the popular coupled‐cluster//Kohn‐Sham density functional theory (CC//KS‐DFT) model chemistry, here applied to study the entrance channel of the reaction, namely by comparing CC//KS‐DFT calculations with KS‐DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS‐DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context. © 2013 Wiley Periodicals, Inc.     

Complexes and clusters of water relevant to atmospheric chemistry: H2O complexes with oxidants.

Experimental observations and data from quantum chemical calculations on complexes between water molecules and small, oxygen-containing inorganic species that play an important role as oxidants in the atmosphere (O(1D), O(3P), O2(X3sigmag), O2(b1sigmag+), O3, HO, HOO, HOOO, and H2O2) are reviewed, with emphasis on their structure, hydrogen bonding, interaction energies, thermodynamic parameters, and infrared spectra. In recent years, weakly bound complexes containing water have increasingly attracted scientific attention. Water in all its phases is a major player in the absorption of solar and terrestrial radiation. Thus, complexes between water and other atmospheric species may have a perceivable influence on the radiative balance and contribute to the greenhouse effect, even though their concentrations are low. In addition, they can play an important role in the chemistry of the Earth's atmosphere, particularly in the oxidation of trace gases. Apart from gas-phase complexes, the interactions of oxidants with ice surfaces have also received considerable advertency lately due to their importance in the chemistry of snow, ice clouds, and ice surfaces (e.g., ice shields in polar regions). In paleoclimate--respectively paleoenvironmental--studies, it is essential to understand the transfer processes from the atmosphere to the ice surface. Consequently, special attention is being paid here to the intercomparison of the properties of binary complexes and the complexes and clusters of more complicated compositions, including oxidants adsorbed on ice surfaces, where ice is considered a kind of large water cluster. Various facts concerning the chemistry of the Earth's atmosphere (concentration profiles and possible influence on radical reactions in the atmosphere) are discussed.     

pKa of acetate in water: a computational study

Several computational methods including the conductor-like polarizable continuum model, CPCM with both UAKS and UAHF cavities, Cramer and Truhlar's generalized Born solvation model, SM5.4(AM1), SM5.4(PM3), and SM5.43R(mPW1PW91/6-31+G(d)), and mixed QM/MM-Ewald simulations were used to calculate the pK(a) values of acetate and bicarbonate anions in aqueous solution. This work provided a critical and comprehensive assessment of the quality of these theoretical models in the calculation of aqueous solvation free energies for the singly charged acetate and bicarbonate ions, as well as the doubly charged acetate dianion and carbonate dianion. It was shown that QM/MM-Ewald simulations could give an accurate and consistent evaluation of the pK(a) values of acetate and bicarbonate based on both the relative and absolute pK(a) formulas, while other methods could yield satisfactory results only for certain calculations. However, this does not mean that the current QM/MM-Ewald protocol is superior to other methods. The useful information obtained in this investigation is that both the absolute and relative pK(a) formulas should better be tested in accurate calculations of pK(a) values based on any methods.     

Water cluster growth in hydrophobic solid nanospaces

The growth mechanism of water clusters in carbon nanopores is clearly elucidated by in situ small-angle X-ray scattering (SAXS) studies and grand canonical Monte Carlo (GCMC) simulations at 293-313 K. Water molecules are isolated from each other in hydrophobic nanopores below relative pressures (P/P(0)) of 0.5. Water molecules associate with each other to form clusters of about 0.6 nm in size at P/P(0)=0.6, accompanied by a remarkable aggregation of these clusters. The complete filling of carbon nanopores finishes at about P/P(0)=0.8. The correlation length analysis of SAXS profiles leads to the proposal of a growth mechanism for these water clusters and the presence of the critical cluster size of 0.6 nm leads to extremely stable clusters of water molecules in hydrophobic nanopores. Once a cluster of the critical size is formed in hydrophobic nanopores, the predominant water adsorption begins to fill carbon nanopores.