Syntheses, crystal and electronic structures, and characterizations of quaternary antiferromagnetic sulfides: Ba2MFeS5 (M = Sb, Bi)

Two new quaternary sulfides, Ba(2)SbFeS(5) and Ba(2)BiFeS(5), were synthesized by using a conventional high-temperature solid-state reaction method in closed silica tubes at 1123 K. The two compounds both crystallize in the orthorhombic space group Pnma with a = 12.128(6) ?, b = 8.852(4) ?, c = 8.917(4) ?, and Z = 4 for Ba(2)SbFeS(5) and a = 12.121(5) ?, b = 8.913(4) ?, c = 8.837(4) ?, and Z = 4 for Ba(2)BiFeS(5). The crystal structure unit can be viewed as an infinite one-dimensional edge-shared MS(5) (M = Sb, Bi) tetragonal-pyramid chain with FeS(4) tetrahedra alternately arranged on two sides of the MS(5) polyhedral chain via edge-sharing (so the chain can also be written as (1)(∞)[MFeS(5)](4-)). Interestingly, the compounds have the structural type of a Ba(3)FeS(5) high-pressure phase considering one Ba(2+) is replaced by one Sb(3+)/Bi(3+), with Fe(4+) reduced to Fe(3+) for in order to maintain the electroneutrality of the system. As a result, the isolated iron ions in Ba(3)FeS(5) are bridged by intermediate MS polyhedra in Ba(2)MFeS(5) (M = Sb, Bi) compounds and form the (1)(∞)[MFeS(5)](4-) chain structure. This atom substitution of Ba(2+) by one Sb(3+)/Bi(3+) leads to a magnetic transition from paramagnetic Ba(3)FeS(5) to antiferromagnetic Ba(2)MFeS(5), resulting from an electron-exchange interaction of the iron ions between inter- or intrachains. Magnetic property measurements indicate that the two compounds are both antiferromagnetic materials with Ne?el temperatures of 13 and 35 K for Ba(2)SbFeS(5) and Ba(2)BiFeS(5), respectively. First-principles electronic structure calculations based on density functional theory show that the two compounds are both indirect-band semiconductors with band gaps of 0.93 and 1.22 eV for Ba(2)SbFeS(5) and Ba(2)BiFeS(5), respectively.     

Assignment of the photoelectron spectra of FeS3(-) by density functional theory, CASPT2, and RCCSD(T) calculations

The geometric structures of FeS(3) and FeS(3)(-) with spin multiplicities ranging from singlet to octet were optimized at the B3LYP level, allowing two low-lying conformations for these clusters to be identified. The planar D(3h) conformation contains three S(2-) atomic ligands (S(3)Fe(0/-)), whereas the C(2v) structure contains, in addition to an atomic S(2-) ligand, also a S(2)(2-) ligand that is side-on-bound to the iron cation: an η(2)-S(2)FeS conformation. Subsequently, energy differences between the various states of these conformations were estimated by carrying out geometry optimizations at the multireference CASPT2 level. Several competing structures for the ground state of the anionic cluster were recognized at this level. Relative stabilities were also estimated by performing single-point RCSSD(T) calculations on the B3LYP geometries. The ground state of the neutral complex was unambiguously found to be (5)B(2). The ground state of the anion is considerably less certain. The 1(4)B(2), 2(4)B(2), (4)B(1), and (6)A(1) states were all found as low-lying η(2)-S(2)FeS(-) states. Also, (4)B(2) of S(3)Fe(-) has a comparable CASPT2 energy. In contrast, B3LYP and RCCSD(T) mutually agree that the S(3)Fe(-) state is at a much higher energy. Energetically, the bands of the photoelectron spectra of FeS(3)(-) are reproduced at the CASPT2 level as ionizations from either the (4)B(2) or (6)A(1) state of η(2)-S(2)FeS. However, the Franck-Condon factors obtained from a harmonic vibrational analysis at the B3LYP level show that only the (4)B(2)-to-(5)B(2) ionization, which preserves the η(2)-S(2)Fe-S conformation, provides the best vibrational progression match with the X band of the experimental photoelectron spectra.     

Layered and pillared metal carboxyethylphosphonate hybrid compounds

A series of carboxyethylphosphonate hybrid materials has been prepared: Mn(II)(O3PCH2CH2COOH) *H2O (1), Mn(III)(OH)(O3PCH2CH2COOH)*H2O (2), Al3(III)(OH)3(O3PCH2CH2CO2)2 *3H2O (3) and Cr2(III)(OH)3(O3PCH2CH2CO2) *3H2O (4). Compounds 1 and 2 were synthesized from Mn(III)(CH3COO)3 *2H2O under hydrothermal, or refluxing treatments, respectively. The crystal structures of the manganese-bearing solids have been solved ab initio from laboratory X-ray powder diffraction data and refined by the Rietveld method. 1 crystallises in a orthorhombic cell and 2 in monoclinic symmetry. Both solids have inorganic 2D layered structures with the acid carboxylic groups pointing towards the interlayer space, and the layers linked only through hydrogen bonds. The inorganic layers of these compounds are formed by manganese atoms in distorted octahedral environments linked together by the phosphonate groups. The crystal structure of 3 has been solved ab initio from synchrotron X-ray powder diffraction data. This solid shows a pillared structure with the phosphonate and carboxylate groups cross-linking the inorganic layers. These layers contain chains of aluminium octahedra running parallel to each other. 4 is amorphous and the IR-UV-VIS spectra suggest a framework with Cr(III) cations in octahedral environments. Thermal, spectroscopic and magnetic data for manganese and chromium compounds as well as the structural details of these solids are discussed.     

Syntheses, structure, and a Mössbauer and magnetic study of Ba(4)Fe(2)I(5)S(4)

The compound Ba4Fe2I5S4 has been prepared at 1223-1123 K by the "U-assisted" reaction of FeS, BaS, S, and U with BaI2 as a flux. A more rational synthesis was also found; however, the presence of U appears to be essential for the formation of single crystals suitable for X-ray diffraction studies. Ba4Fe2I5S4 crystallizes in a new structure type with two formula units in space group I4/m of the tetragonal system. The structure consists of a Ba-I network penetrated by (1)infinity[Fe2S4] chains. Each Fe atom, which is located on a site with 4 symmetry, is tetrahedrally coordinated to four S atoms. The FeS4 tetrahedra edge-share to form linear (1)infinity[Fe2S4] chains in the [001] direction. The Fe-Fe interatomic distance in these chains is 2.5630(4) A, only about 3% longer than the shortest Fe-Fe distance in -Fe metal. Charge balance dictates that the average formal oxidation state of Fe in these chains is +2.5. The M?ssbauer spectra obtained at 85 and 270 K comprise a single quadrupole doublet that has hyperfine parameters consistent with an average Fe oxidation state of +2.5. The M?ssbauer spectrum obtained at 4.2 K consists of a single magnetic sextet with a small hyperfine field of -15.5 T. This spectrum is also consistent with rapid electron delocalization and an average Fe oxidation state of +2.5. The molar magnetic susceptibility of Ba4Fe2I5S4, obtained between 3.4 and 300 K, qualitatively indicates the presence of weak pseudo-one-dimensional ferromagnetic exchange within a linear chain above 100 K and weak three-dimensional ordering between the chains at lower temperatures.     

Interpretation of the photoelectron spectra of FeS(2)(-) by a multiconfiguration computational approach

The ground states of FeS(2) and FeS(2)(-), and several low-lying excited electronic states of FeS(2) that are responsible for the FeS(2)(-) photoelectron spectrum, are calculated. At the B3LYP level an open, quasi-linear [SFeS](-) conformation is found as the most stable structure, which is confirmed at the ab initio CASPT2 computational level. Both the neutral and the anionic unsaturated complexes possess high-spin electronic ground states. For the first time a complete assignment of the photoelectron spectrum of FeS(2)(-) is proposed. The lowest energy band in this spectrum is ascribed to an electron detachment from the two highest-lying 3dpi antibonding orbitals (with respect to the iron-sulfur bonding) of iron. The next-lowest experimental band corresponds to an electron removal from nonbonding, nearly pure sulfur orbitals. The two highest bands in the spectra are assigned as electron detachments from pi and sigma bonding mainly sulfur orbitals.     

Theoretical analysis of the Jahn-Teller distortions in tetrathiolato iron(II) complexes

Crystallographic studies of [Fe(SR)(4)](2-) (R is an alkyl or aryl residue) have shown that the Fe(II)S(4) cores of these complexes have (pseudo) D2d symmetry. Here we analyze the possibility that these structures result from a Jahn-Teller (JT) distortion that arises from the e(3z(2) - r(2), x(2) - y(2)) orbital ground state of Fe(II) in T(d)symmetry. Special attention is paid to the influence of the second-nearest neighbors of Fe, which lowers the symmetry and reduces the full JT effect to a smaller, pseudo JT effect (PJT). To estimate the size of the PJT distortion, we have determined the vibronic parameters and orbital state energies for a number of [Fe(SR)(4)](2-) models using density functional theory (DFT). Subsequently, this information is used for evaluating the adiabatic potential surfaces in the space of the JT-active coordinates of the FeS(4) moiety. The surfaces reveal that the JT effect of Fe(II) is completely quenched by the tetrathiolate coordination.     

Determination of FeS(2) in Venezuelan laterites after a sulphurization process

A technique is presented for determination of FeS(2) in Venezuelan laterites after a sulphurization process. The determination is based on a reaction with water followed by a turbidimetric determination of sulphate ions in solution. The effect of the reaction time and of the particle size is investigated. Data are given showing the precision to be better than 3%, and the accuracy was studied by preparation of a series of synthetic samples of FeS(2), FeS and Venezuelan laterite.     

铁硫蛋白活性中心铁硫簇的对称性破缺密度泛函 计算

应用密度泛函方法(DFT)计算了铁硫金属蛋白中的铁硫簇[Fe~2S~2(SCH~3)~4]^2^-,[Fe~3S~4(SCH~3)~3]^2^-以及[Fe~4S~4(SCH~3)~4]^2^-的几何参数和磁偶合性质。采用对称性破缺态(BS)来描述Fe－Fe自旋偶合。计算结果表明：采用高自旋态(HS)计算的Fe－Fe间距与实验值有较大偏差,而由BS方法所计算的Fe－Fe间距与晶体结构测定数据相吻合。根据HS态和BS态的能量,计算了体系的海森堡偶合参数J,计算结果也较为接近实验估算值。     

Molybdenum-iron-sulfur clusters of nuclearities eight and sixteen, including a topological analogue of the P-cluster of nitrogenase

Transformations of the edge-bridged double cubane cluster [(Cl4cat)2(Et3P)2Mo2Fe6S8(PEt3)4] (1) under reducing conditions have been investigated as synthetic approaches to the clusters of nitrogenase. Cluster 1 is a versatile precursor to different Mo-Fe-S cluster types. The reaction system 1/K(C14H10) in THF yields the reduced cluster [(Cl4cat)2(Et3P)2Mo2Fe6S8(PEt3)4]1- (2), which as its crystalline Et4N+ salt retains the edge-bridged structure of 1. X-ray structural and M?ssbauer spectroscopic results indicate an unsymmetrical electron distribution with localized [MoFe3S4]2+,1+ cubane-type units. The system 1/2K(C14H10)/2HS- in THF/acetonitrile affords [(Cl4cat)4(Et3P)4Mo4Fe12S20K3(DMF)]5- (3), whose structure was determined as the Ph3PMe+ salt. The cluster consists of two isostructural Mo2Fe6S9 fragments connected by two mu 2-S bridges. Three potassium ions are bound between the two fragments. In each fragment, the iron atoms are present in tetrahedral FeS4 and the molybdenum atoms in octahedral MoO2PS3 coordination units, and two MoFe3(mu 3-S)3 cuboidal units are bridged by a common mu 6-S atom. The fragments have idealized mirror symmetry and are isostructural with two of the fragments present in the previously reported high-nuclearity cluster [(Cl4cat)6(Et3P)6Mo6Fe20S30]8- (4) (Osterloh, F.; Sanakis, Y.; Staples, R. J.; Münck, E.; Holm, R. H. Angew. Chem., Int. Ed. Engl. 1999, 38, 2066). On the basis of overall shape, atom connectivities, and metric features, the Mo2Fe6S9 fragment is a topological analogue of the P-cluster of nitrogenase in the PN (reduced) state. A third cluster type, formed as a minor byproduct in the reaction system leading to 2, was crystallographically identified as [(Cl4cat)2(Et3P)2Mo2Fe6S8(PEt3)4]4-, whose core is made up of two MoFe3(mu 3-S)3 cuboidal units bridged by two mu 2-S atoms and connected by a direct Fe-Fe bond. Full structural details and the redox properties of 2 and 3 are reported.     

Phase-selective chemical extraction of selenium and sulfur from nanoscale metal chalcogenides: a general strategy for synthesis, purification, and phase targeting

Controlling the composition and phase formation of bulk and nanoscale solids underpins efforts to control physical properties. Here, we introduce a powerful new chemical pathway that facilitates composition-tunable synthesis, post-synthesis purification, and precise phase targeting in metal chalcogenide systems. When metal selenides and sulfides react with trioctylphosphine (TOP) at temperatures that range from 65 to 270 °C, selenium and sulfur are selectively extracted to produce the most metal-rich chalcogenide that is stable in a particular binary system. This general approach is demonstrated for SnSe(2), FeS(2), NiSe(2), and CoSe(2), which convert to SnSe, FeS, Ni(3)Se(2), and Co(9)Se(8), respectively. In-depth studies of the Fe-Se system highlight the precise phase targeting and purification that is achievable, with PbO-type FeSe (the most metal-rich stable Fe-Se phase) forming exclusively when other Fe-Se phases, including mixtures, react with TOP. This chemistry also represents a new template-based nanoparticle "conversion chemistry" reaction, transforming hollow NiSe(2) nanospheres into hollow NiSe nanospheres with morphological retention.     

Theoretical Study on the Reaction of FeS+(6∑+,4Ф)with COS in the Gas Phase

The possible reaction mechanisms of FeST(6∑+and 4Ф states)with COS in the gas phase have been studied by using density functional theory at the B3LYP/TZVP and B3LYP/6-311+G*levels:the O/S exchange reaction(FeS++COS=FeO++CS2),O-transfer reaction(FeS++COS=FeSO++CS)and S-transfer reaction(FeS++COS=FeS2++CO).The calculation results show that the large barriers(205.7 and 310.1 kJ/mol)and the small probability of forming the preceding intermediate indicate a much lower efficiency of the O/S exchange and the O-transfer reactions and their corresponding products may not be observed experimentally.FeS2+,the product of S-transfer reaction,is predicted to be the main product.But the reactivity of the 6∑+ground state of FeS+toward COS is lower than the earlier transition metal sulfide cations MS+(M=Sc,Ti and V),although it has more reaction channels and different mechanisms.     

High-nuclearity sulfide-rich molybdenum[bond]iron[bond]sulfur clusters: reevaluation and extension

High-nuclearity Mo[bond]Fe[bond]S clusters are of interest as potential synthetic precursors to the MoFe(7)S(9) cofactor cluster of nitrogenase. In this context, the synthesis and properties of previously reported but sparsely described trinuclear [(edt)(2)M(2)FeS(6)](3-) (M = Mo (2), W (3)) and hexanuclear [(edt)(2)Mo(2)Fe(4)S(9)](4-) (4, edt = ethane-1,2-dithiolate; Zhang, Z.; et al. Kexue Tongbao 1987, 32, 1405) have been reexamined and extended. More accurate structures of 2-4 that confirm earlier findings have been determined. Detailed preparations (not previously available) are given for 2 and 3, whose structures exhibit the C(2) arrangement [[(edt)M(S)(mu(2)-S)(2)](2)Fe(III)](3-) with square pyramidal Mo(V) and tetrahedral Fe(III). Oxidation states follow from (57)Fe M?ssbauer parameters and an S = (3)/(2) ground state from the EPR spectrum. The assembly system 2/3FeCl(3)/3Li(2)S/nNaSEt in methanol/acetonitrile (n = 4) affords (R(4)N)(4)[4] (R = Et, Bu; 70-80%). The structure of 4 contains the [Mo(2)Fe(4)(mu(2)-S)(6)(mu(3)-S)(2)(mu(4)-S)](0) core, with the same bridging pattern as the [Fe(6)S(9)](2-) core of [Fe(6)S(9)(SR)(2)](4-) (1), in overall C(2v) symmetry. Cluster 4 supports a reversible three-member electron transfer series 4-/3-/2- with E(1/2) = -0.76 and -0.30 V in Me(2)SO. Oxidation of (Et(4)N)(4)[4] in DMF with 1 equiv of tropylium ion gives [(edt)(2)Mo(2)Fe(4)S(9)](3-) (5) isolated as (Et(4)N)(3)[5].2DMF (75%). Alternatively, the assembly system (n = 3) gives the oxidized cluster directly as (Bu(4)N)(3)[5] (53%). Treatment of 5 with 1 equiv of [Cp(2)Fe](1+) in DMF did not result in one-electron oxidation but instead produced heptanuclear [(edt)(2)Mo(2)Fe(5)S(11)](3-) (6), isolated as the Bu(4)N(+)salt (38%). Cluster 6 features the previously unknown core Mo(2)Fe(5)(mu(2)-S)(7)(mu(3)-S)(4) in molecular C(2) symmetry. In 4-6, the (edt)MoS(3) sites are distorted trigonal bipramidal and the FeS(4) sites are distorted tetrahedral with all sulfide ligands bridging. M?ssbauer spectroscopic data for 2 and 4-6 are reported; (mean) iron oxidation states increase in the order 4 < 5 approximately 1 < 6 approximately 2. Redox and spectroscopic data attributed earlier to clusters 2 and 4 are largely in disagreement with those determined in this work. The only iron and molybdenum[bond]iron clusters with the same sulfide content as the iron[bond]molybdenum cofactor of nitrogenase are [Fe(6)S(9)(SR)(2)](4-) and [(edt)(2)Mo(2)Fe(4)S(9)](3-)(,4-).     

Solid memory: structural preferences in group 2 dihalide monomers, dimers, and solids

The link between structural preferences in the monomers, dimers, and extended solid-state structures of the group 2 dihalides (MX(2): M = Be, Mg, Ca, Sr, Ba and X = F, Cl, Br, I) is examined theoretically. The question posed is how well are geometric properties of the gas-phase MX(2) monomers and lower order oligomers "remembered" in the corresponding MX(2) solids. Significant links between the bending in the MX(2) monomers and the D(2)(h)()/C(3)(v)() M(2)X(4) dimer structures are identified. At the B3LYP computational level, the monomers that are bent prefer the C(3)(v)() triply bridged geometry, while the rigid linear molecules prefer a D(2)(h)() doubly bridged structure. Quasilinear or floppy monomers show, in general, only a weak preference for either the D(2)(h)() or the C(3)(v)() dimer structure. A frontier orbital perspective, looking at the interaction of monomer units as led by a donor-acceptor interaction, proves to be a useful way to think about the monomer-oligomer relationships. There is also a relationship between the structural trends in these two (MX(2) and M(2)X(4)) series of molecular structures and the prevalent structure types in the group 2 dihalide solids. The most bent monomers condense to form the high coordination number fluorite and PbCl(2) structure types. The rigidly linear monomers condense to form extended solids with low coordination numbers, 4 or 6. The reasons for these correlations are explored.     

Atom-centered symmetry functions for constructing high-dimensional neural network potentials

Neural networks offer an unbiased and numerically very accurate approach to represent high-dimensional ab initio potential-energy surfaces. Once constructed, neural network potentials can provide the energies and forces many orders of magnitude faster than electronic structure calculations, and thus enable molecular dynamics simulations of large systems. However, Cartesian coordinates are not a good choice to represent the atomic positions, and a transformation to symmetry functions is required. Using simple benchmark systems, the properties of several types of symmetry functions suitable for the construction of high-dimensional neural network potential-energy surfaces are discussed in detail. The symmetry functions are general and can be applied to all types of systems such as molecules, crystalline and amorphous solids, and liquids.     

One-step synthesis of cubic FeS2 and flower-like FeSe2 particles by a solvothermal reduction process

In this paper, for the first time a simple batch process was utilized for the facile synthesis of cubic FeS(2) and flower-like FeSe(2). By adjusting the amount of solvents and surfactants added, pure pyrite FeS(2) with a defined crystalline structure was obtained. It was found that the reaction temperatures and iron sources had significant influence on the purities and morphologies of FeS(2) and FeSe(2) particles. Raman spectra of the FeS(2) and FeSe(2) samples presented characteristic peaks of S-S and Se-Se active modes at 337, 372 cm(-1), and 180, 217, 254 cm(-1), respectively. The absorption properties of the FeS(2) and FeSe(2) samples were also investigated and the results demonstrated that these samples had broad optical absorption in NIR. Moreover, the synthetic approach demonstrated here may be of great potential for the controlled synthesis of other metal chalcogenides.     

Iron monosulfide (FeS) oxidation by dissolved oxygen: characteristics of the product layer

Samples of FeS were oxidized by oxygen‐bearing acidic solutions at 25 °C and different initial pH values (2.75 ≤ pH ≤ 3.45). The reacted FeS samples were investigated by scanning electron microscopy (SEM), nitrogen adsorption/desorption isotherms measurements, and FT‐Raman spectroscopy. A sulfur rich phase (layer) is inferred to be form on reacting FeS surface based on sequential extraction with acidic chromium(II) chloride solutions. The sulfur‐rich layer (SRL) formed on oxidized FeS samples is traversed by various mesopores with average pore size < 450Å. It is reasonable to assume that the mesopores facilitate the migration of iron and sulfur from FeS structure into solution across SRL. The FT‐Raman spectra of oxidized FeS samples show an intense peak at 162 cm^?1, which can be attributed to SRL developed on FeS surface. A model for SRL development on FeS during its oxidation by dissolved oxygen has been proposed from the present results and previous studies. Copyright © 2009 John Wiley & Sons, Ltd.     

Zirconium hydrocarbyl chemisorption on sulfated metal oxides: new supports, chemisorption pathways, and implications for catalysis

The sulfated metal oxides (SMOs) sulfated stannia (SnS), sulfated iron oxide (FeS), and sulfated titanium dioxide (TiS) have been synthesized and examined as support materials/cocatalysts/activators for molecule-based olefin polymerization and hydrogenation catalysis. (13)C CPMAS NMR spectroscopic analysis of Cp(2)Zr((13)CH(3))(2)/SMO chemisorption shows that cationic zirconocenium species are formed along with varying amounts of catalytically inactive micro-oxo (Cp(2)Zr(CH(3))O-surface) species, depending on the support material. Ethylene polymerization data with the supported catalysts show that polymerization activity is dependent on both precursor ligation [Zr(CH(2)Ph)(4) > (Me(5)Cp)ZrMe(3)] and the nature of the support (SnS > FeS > TiS). Poisoning studies were performed in conjunction with ethylene polymerization, mediated by (Me(5)Cp)ZrMe(3) supported on each SMO, and reveal that, for (Me(5)Cp)ZrMe(3)/SnS, 61 +/- 5% of the Zr sites are catalytically significant, while, for (Me(5)Cp)ZrMe(3)/FeS, this quantity is 22 +/- 2%, and for (Me(5)Cp)ZrMe(3)/TiS, 63 +/- 9%. These catalysts are also active for benzene hydrogenation and are separable from liquid-phase products using physical or, in the case of FeS, magnetic techniques.     

A Crystal Orbital approach for two- and three-dimensional solids on the basis of CNDO/INDO Hamiltonians. Basis equations

A Hartree–Fock (HF ) self-consistent field (SCF ) crystal orbital (CO ) formalism for two- and three-dimensional (2D/3D) solids on the basis of semiempirical CNDO /INDO (complete neglect of differential overlap; intermediate neglect of differential overlap) Hamiltonians is presented. The employed SCF variants allow for the treatment of atomic species up to bromine under the inclusion of the first (i.e., 3d) transition metal series. Band structure investigations of 2D and 3D materials containing more than 30 atoms per unit cell are feasible by the present SCF HF CO formalism. The theoretical background of the computational scheme is given in this contribution. Special emphasis is placed on physically reliable truncation criteria for the lattice sums, the adaptation of the crystal symmetry in k space, as well as the suitable choice of domains in Brillouin zone (BZ ) integrations required in the determination of charge-density matrices. The capability and limitations of the semiempirical SCF HF CO approach is demonstrated for some simpler solids by comparing the present computational results with those of ab initio CO schemes as well as conventional numerical methods in soid-state theory. The employed model solids are graphite and BN (2D and 3D networks for both solids) as well as diamond, silicon, germanium, and TiS₂.     

Structures of water octamers (H2O)8: exploration on ab initio potential energy surfaces by the scaled hypersphere search method

The potential energy surface (PES) of water octamers has been explored by the scaled hypersphere search method. Among 164 minima on the PES (based on MP2/6-311++G(3df,2p)//B3LYP/6-311+G(d,p) calculations), the cubic structure with D2d symmetry has been confirmed to be the global minimum. In a thermodynamic simulation using these 164 structures, the cubic structure with S4 symmetry has the highest population at low temperature, though double rings can become dominant as temperature going up, in good accord with a recent Monte Carlo simulation using an empirical potential. A transition temperature from cubic to noncubic has significantly been underestimated when potential energy data of B3LYP/6-311+G(d,p) calculations are employed in the simulation. This serious discrepancy between the MP2 and the B3LYP results suggests an importance of dispersion interactions for discussions on thermodynamics of water octamers.     

Practical modeling of molecular systems with symmetries

A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree‐based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree‐based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010