Water tetramer, pentamer, and hexamer in inert matrices

The infrared spectrum of water, isolated in inert matrices, has been studied in the interval from 60 to 4000 cm(-1). Experiments with partially deuterated water combined with DFT (density functional theory) calculations have been used to investigate the structure of matrix-isolated water tetramer. A few, strong intermolecular fundamentals of the water tetramer have been observed. Mid-infrared bands due to deuterated pentamers and hexamers have been observed and are used to discuss the assignments of these water clusters.     

Fundamentals and application of ordered molecular assemblies to affinity biosensing

Organization of biomolecules in two/three dimensional assemblies has recently aroused much interest in nanobiotechnology. In this context, the development of techniques for controlling spatial arrangement and orientation of the desired molecules to generate highly-ordered nanostructures in the form of a mono/multi layer is considered highly significant. The studies of monolayer films to date have focused on three distinct methods of preparation: (i) the Langmuir-Blodgett (LB) technique, involving the transfer of a monolayer assembled at the gas-liquid interface; (ii) self-assembly at the liquid-solid interface, based on spontaneous adsorption of desired molecules from a solution directly onto a solid surface; and (iii) Layer-by-layer (LBL) self-assembly at a liquid-solid interface, based on inter-layer electrostatic attractions for fabrication of multilayers. A variety of monolayers have been utilized to fabricate biomolecular electronic devices including biosensors. The composition of a monolayer based matrix has been found to influence the activity(ies) of biomolecule(s). We present comprehensive and critical analysis of ordered molecular assemblies formed by LB and self-assembly with potential applications to affinity biosensing. This critical review on fundamentals and application of ordered molecular assemblies to affinity biosensing is likely to benefit researchers working in this as well as related fields of research (401 references).     

Structural and dynamical properties of water dimer and tetramer: molecular dynamics study

A detailed evaluation of the structural and dynamical properties of isolated water dimers and tetramers using the Lemberg, Stillinger and Rahman potential energy surface and microcanonical molecular dynamics simulations are reported. The lowest-energy configurations of these clusters were obtained by simulated thermal quenching. Relative root-mean-square bond length fluctuations were used to characterize phase transitions. Solid-like, pre-melting, liquid-like, and dissociated states were identified. Global-local minimum transitions and the minimum energy path to dissociation of the dimer were also characterized.     

Structural characterization of a procyanidin tetramer and pentamer from the apple by low-temperature NMR analysis

The structures of a procyanidin tetramer and pentamer from unripe apple (Malus pumila) were elucidated by low-temperature NMR analysis at −34 °C. These structures were [epicatechin-(4β→6)-epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin (1)] and [epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin-(4β→8)-epicatechin (2)].     

Reactions of tetrafluoroethylene oligomers. Part 1. Some pyrolytic reactions of the pentamer and hexaher and of the fluorine adducts of the tetramer and pentamer

Pyrolyses of these highly branched fluorocarbons over glass beads caused the preferential thermolyses of CC bonds where there is maximum carbon substitution. Fluorinations of perfluoro-3,4-dimethylhex-3-ene (tetramer) (I) and perfluoro-4-ethyl-3,4-dimethylhex- 2-ehe (pentamer) (II) over cobalt (III) fluoride at 230° and 145° respectively afforded the corresponding saturated fluorocarbons (III) and (IV), though II gave principally the saturated tetramer (III) at 250°. Pyrolysis of III alone at 500—520° gave perfluoro-2-methylbutane (V), whilst pyrolysis of III in the presence of bromine or toluene afforded 2-bromononafluorobutane (VI) and 2H-nonafluorobutane (VII) respectively. Pyrolysis of perfluoro-3-ethyl-3, 4-dimethylhexane (IV) alone gave a mixture of perfluoro-2-methylbutane (V), perfluoro-2-methylbut-1-ene (VIII), perfluoro-3-methylpentane (IX), perfluoro-3,3-dimethylpentane (X), and perfluoro-3,4- dimethylhexane (III). Pyrolysis of IV in the presence of bromine gave (VI) and 3-bromo-3-trifluoromethyl-decafluoropentane (XI): with toluene, pyrolysis gare VlI and 3H-3-trifluoromethyldecafluoropentane (XII). Pyrolysis of II at 500° over glass gave perfluoro-1,2,3-trimethylcyclobutene (XIII) and perfluoro-2,3-dimethylpenta-1,3(E)- and (Z)-diene (XIV) and (XV) respectively. The diene mixture (XIV and XV) was fluorinated with CoF₃ to give perfluoro-2,3-dimethylpentane (XVI) and was cyclised thermally to give the cyclobutene (XIII). Pyrolysis of perfluoro-2- (1′-ethyl-1′-methylpropyl)-3-methylpent-1-ene (XVII) (TFE hexamer major isomer) at 500° gave perfluoro-1-methyl-2-(1′-methylpropyl)cyclobut-1-ene (XVIII) and perfluoro-2-methyl-2-(1′-methylpropyl)buta-1,3-diene (XIX). Fluorination of XVIII over CoF₃ gave perfluoro-1-methyl-2- (1′-methylpropyl)cyclobutane (XX), which on co-pyrolysis with bromine gave VI. XIX on heating gave XVIII. Reaction of XVIII with ammonia in ether gave a mixture of E and Z 1′-trifluoromethyl-2-(1′-trifluoromethyl- pentafluoropropyliden-1′-yl)tetrafluorocyclobutylamine (XXI) which on diazotisation and hydrolysis afforded 2-(2′trifluoromethyl- tetrafluorocyclobut-1-en-1′-yl)-octafluorobutan-2-ol (XXII).     

Photoinduced electron transfer and solvation dynamics in aqueous clusters: comparison of the photoexcited iodide-water pentamer and the water pentamer anion

Upon photoexcitation of iodide-water clusters, I(-)(H(2)O)(n), an electron is transferred from iodide to a diffuse cluster-supported, dipole-bound orbital. Recent femtosecond photoelectron spectroscopy experiments have shown that, for photoexcited I(-)(H(2)O)(n) (n≥ 5), complex excited-state dynamics ultimately result in the stabilization of the transferred electron. In this work, ab initio molecular dynamics simulations of excited-state I(-)(H(2)O)(5) and (H(2)O)(5)(-) are performed, and the simulated time evolution of their structural and electronic properties are compared to determine unambiguously the respective roles of the water molecules and the iodine atom in the electron stabilization dynamics. Results indicate that, driven by the iodine-hydrogen repulsive interactions, excited I(-)(H(2)O)(5) rearranges significantly from the initial ground-state minimum energy configuration to bind the excited electron more tightly. By contrast, (H(2)O)(5)(-) rearranges less dramatically from the corresponding configuration due to the lack of the same iodine-hydrogen interactions. Despite the critical role of iodine for driving reorganization in excited I(-)(H(2)O)(5), excited-electron vertical detachment energies appear to be determined mostly by the water cluster configuration, suggesting that femtosecond photoelectron spectroscopy primarily probes solvent reorganization in photoexcited I(-)(H(2)O)(5).     

Flip rearrangement in the water pentamer: Analysis of electronic structure

Tunneling pathways of the flip rearrangement between permutation-inversion isomers corresponding to the energetically degenerate global energy minima of (H₂O)₅ are analyzed in terms of the electronic structure. We demonstrate that charge density-based scalar measures quantify the responses of the bonding to the flip rearrangement and we discovered a high degree of continuity of the values that depend on the presence of the sliding motion of the bond critical point relative to the oxygen atom. The scalar measures can distinguish the pairs of permutation-inversion isomers everywhere except at the transition state due to the asymmetrical energy barrier; however, they cannot determine the most and least facile directions of the flip rearrangement. The vector or directional character of the two sides of the pathway is captured by the stress tensor trajectories constructed in a non-Cartesian space, defined by the variation of the position of the bond critical point. The stress tensor trajectories are presented in terms that enable bond-flexing, bond-twist, and bond-anharmonicity of the flip rearrangement between permutation-inversion isomers to be quantified. The stress tensor trajectories can distinguish the isomers at the transition state and demonstrate that the clockwise and counter-clockwise directions of the flip rearrangement are the most and least facile respectively.     

Kinetically forbidden transformations of water molecular assemblies in hydrophobic micropores

Water adsorption hysteresis is one of the most important phenomena observed during the interaction of water with hydrophobic surfaces. Adsorption hysteresis in micropores has strong relevance to the structure of adsorbed water. We used three typical models (cluster, monolayer, and uniform distribution structure models) to determine the structure of the water molecules adsorbed in hydrophobic slit-shaped carbon micropores. In each model, stabilization energy profiles were calculated for various fractional fillings by using the interaction potential theory. Simultaneously, molecular dynamics (MD) simulations of water adsorbed in the micropore of 1.1 nm pore width, which shows significant adsorption hysteresis, were performed to determine the kinetics of the observed structural transformations. The transformations between monolayer and cluster were slow, that is, kinetically forbidden at the fractional filling of 0.2 and 0.6, whereas the cluster-uniform distribution structure and uniform distribution structure-monolayer transformations were kinetically allowed. The kinetically forbidden transformation resulted in the occurrence of metastable structure of adsorbed water and was responsible for the observed adsorption hysteresis.     

On the application of group theory to molecular excitons

In this paper a group theoretical approach was employed for the classification and construction of molecular exciton wavefunctions for two important crystal structures (naphthalene—anthracene and benzene), utilizing the representation theory of finite groups. The generally valid scheme requires only cyclic boundary conditions (being explicitly imposed on all space group operations, including rotations and reflections). Even though these symmetry considerations are insufficient to determine crystal wavefunctions belonging to a general k vector, it is still possible to write a simple expression for such wavefunctions. This is achieved for cases where the nonvanishing exciton transfer integrals are confined to molecular interactions along symmetry axes and/or planes.     

Sequence-adapted molecular tensors: Algebraic methods and application to crystal field theory

Tensorial sets adapted to sequences of finite subgroups are applied to the crystal field problem, and a general method for generating sequence-adapted molecular tensors using finite group algebra is formulated. All subgroup sequences of the abstract finite group G(24), isomorphic to the octahedral, O, tetrahedral, T_d, and symmetric, S(4), groups are tabulated with explicit isomorphisms provided. The sequences fall into eight equivalence classes. A catalog of irreducible representations of G(24) adapted to a member of each of the eight sequence classes is given together with the transformations which generate representations adapted to all other sequences. With this data it is possible to systematically generate tensorial sets adapted to any sequence of a realization of G(24). Unitary transformations which adapt conventional forms of first- and second-rank irreducible tensorial sets of the rotation group to the eight sequences of the octahedral group are provided. Forms suitable for use with magnetic fields are included. The problem of a d¹ ion in a trigonal crystal field is treated with sequence-adapted molecular tensors, and the utility of different sequences for descent in symmetry is discussed.     

An evolutionary algorithm for the global optimization of molecular clusters: application to water, benzene, and benzene cation

We have developed an evolutionary algorithm (EA) for the global minimum search of molecular clusters. The EA is able to discover all the putative global minima of water clusters up to (H(2)O)(20) and benzene clusters up to (C(6)H(6))(30). Then, the EA was applied to search for the global minima structures of (C(6)H(6))(n)(+) with n = 2-20, some of which were theoretically studied for the first time. Our results for n = 2-6 are consistent with previous theoretical work that uses a similar interaction potential. Excluding the very symmetric global minimum structure for n = 9, the growth pattern of (C(6)H(6))(n)(+) with n ≥ 7 involves the (C(6)H(6))(2)(+) dimer motif, which is placed off-center in the cluster. Such observation indicates that potentials commonly used in the literature for (C(6)H(6))(n)(+) cannot reproduce the icosahedral-type packing suggested by the available experimental data.     

An efficient methodology to study cyclodextrin clusters: application to α-CD hydrated monomer, dimer, trimer and tetramer

The hydrated α-cyclodextrin (α-CD) clusters resulting from the following process: nα-CD + n(H₂O)₆ → α-CD_n · 6nH₂O, with n = 1, 2, 3, 4, have been investigated using semiempirical (PM3), ab initio Hartree-Fock and Density Functional Theory (BLYP functional) levels of theory. The largest structure containing 576 atoms and 5,760 contracted basis functions (6-31G(d,p) basis set) poses as a considerable hard task for quantum chemical calculations. As the number of basis function increases rapidly with the cluster size, an alternative procedure to make the calculations feasible is certainly welcome, in order to perform BLYP calculations with an adequate basis set. Through the aid of a computer program that we developed, it became of practical use the selection of atom by atom basis sets, using the common chemical sense, enabling quantum mechanical calculations to be performed for very large molecular interacting systems (inclusion complexes), at an affordable computational cost. In this article we show how an appropriate selection of basis functions, leaving the CH_n groups with a minimal basis set and the oxygen atoms (and OH groups) with a better quality basis set, lower considerably the computational cost with no significant loss in the calculated interaction energies. A regular pattern is observed for α-CD hydrated monomer, dimer, trimer and tetramer, therefore adding support to the use of this procedure when studying larger hydrogen bonded clusters where electron correlation effects are important. We show that the procedure reported here enables DFT calculations for hydrated cyclodextrin using basis set up to the 6-311++G(3df,3pd) triple zeta quality .     

The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies

The modification of surfaces with self-assembled monolayers (SAMs) containing multiple different molecules, or containing molecules with multiple different functional components, or both, has become increasingly popular over the last two decades. This explosion of interest is primarily related to the ability to control the modification of interfaces with something approaching molecular level control and to the ability to characterise the molecular constructs by which the surface is modified. Over this time the level of sophistication of molecular constructs, and the level of knowledge related to how to fabricate molecular constructs on surfaces have advanced enormously. This critical review aims to guide researchers interested in modifying surfaces with a high degree of control to the use of organic layers. Highlighted are some of the issues to consider when working with SAMs, as well as some of the lessons learnt (169 references).     

Quantum diffusion in liquid water from ring polymer molecular dynamics

We have used the ring polymer molecular-dynamics method to study the translational and orientational motions in an extended simple point charge model of liquid water under ambient conditions. We find, in agreement with previous studies, that quantum-mechanical effects increase the self-diffusion coefficient D and decrease the relaxation times around the principal axes of the water molecule by a factor of around 1.5. These results are consistent with a simple Stokes-Einstein picture of the molecular motion and suggest that the main effect of the quantum fluctuations is to decrease the viscosity of the liquid by about a third. We then go on to consider the system-size scaling of the calculated self-diffusion coefficient and show that an appropriate extrapolation to the limit of infinite system size increases D by a further factor of around 1.3 over the value obtained from a simulation of a system containing 216 water molecules. These findings are discussed in light of the widespread use of classical molecular-dynamics simulations of this sort of size to model the dynamics of aqueous systems.     

para-Acylcalix[n]arenes: from molecular to macroscopic assemblies

The para-acylcalix[n]arenes possess a very rich capacity to self-assemble into a wide variety of structures and sizes ranging from molecular assemblies through dimeric capsules, molecular sheets to nanoparticles. All these assemblies are capable of taking guest molecules and in the process of this inclusion discrete nanoscopic reaction vessels may be formed for photochemistry. Interestingly this uptake of quite large organic molecules occurs in the bulk in non-porous crystals without loss of crystallinity. At the air-water interface either as Langmuir monolayers or as colloidal suspensions the para-acylcalix[n]arenes show interaction with ionic species. The extension from para-acylcalix[4]arenes to para-acylcalix[8]arenes is in its infancy but already there is much promise for novel assemblies to be found.     

Utilization of deformations in molecular quantum chemistry and application to density functional theory

The aim of this article is to present in a way accessible to most quantum chemists a general mathematical method which consists in deforming wave functions and density functions (in the spirit of the local scaling transformation). This deformation method allows us to obtain several new results, including a characterization of the set of wave functions that have the same given density function (which gives a new insight on a result of G. Zumbach and K. Maschke, Phys. Rev. A 28 , 544 (1983)) and an N-representability result where symmetry is taken into account. We also propose new theoretical ways to generate approximations of the exact density functional and give a numerical example. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 221–231, 1998     

On the application of accelerated molecular dynamics to liquid water simulations

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.     

Novel water clusters in the crystalline state: structures of a symmetrical,cyclic hexamer and an 'opened-cube' octamer

Six- and eight-membered hydrogen-bonded water clusters of novel structure types have been found in crystalline hydrates.     

Crystal and molecular structures of ionophore-siderophore host-guest supramolecular assemblies relevant to molecular recognition

Ionophore-siderophore host-guest assemblies composed of 18-crown-6 and ferrioxamine B, benzo-18-crown-6 and ferrioxamine B, and cis-syn-cis-dicyclohexano-18-crown-6 and ferrioxamine B were successfully crystallized, and their structures were determined by single-crystal X-ray diffraction. All three crystal lattices also include solvated Mg(II) and perchlorate ions. The ionophore-siderophore host-guest assembly is noncovalently held together by a hydrogen bonding interaction between the pendant protonated amine in the second coordination sphere of ferrioxamine B and the hydrogen bond acceptor oxygen atoms in the crown ether. The crystals of 18-crown-6:ferrioxamine B host-guest assembly are monoclinic, with space group P2(1)/c, and four molecules per unit cell with dimensions a = 19.8327(11) A, b = 20.4111(11) A, c = 15.1698(8) A, and beta = 96.435(1) degrees. The crystals of benzo-18-crown-6:ferrioxamine B host-guest assembly are triclinic, with space group P(-)1, and two molecules per unit cell with dimensions a = 11.1747(10) A, b = 16.0580(15) A, c = 18.4175(17) A, alpha = 80.469(3) degrees, beta = 81.481(3) degrees and gamma = 70.212(2) degrees. The crystals of cis-syn-cis-dicyclohexano-18-crown-6:ferrioxamine B host-guest assembly are monoclinic, with space group P2(1)/c, and four molecules per unit cell with dimensions a = 20.1473(13) A, b = 21.5778(15) A, c = 14.8013(10) A, and beta = 94.586(2) degrees. The crystal structures of all three host-guest assemblies contain a racemic mixture of Lambda-N-cis, cis and Delta-N-cis, cis coordination isomers of ferrioxamine B. The crystal structures indicate that the steric rigidity of the benzo-18-crown-6 and cis-syn-cis-dicyclohexano-18-crown-6 cavity has a pronounced effect on the conformation of the crown ring and ultimately on the hydrogen bonding interactions between the crown ethers and ferrioxamine B. The structural parameters and the conformational features of the ferrioxamine B guests compare very well with each other and with those of the ferrioxamine B structure obtained in the absence of a host. Structural features relevant to siderophore molecular recognition are discussed.