How Inert, Perturbing, or Interacting Are Cryogenic Matrices? A Combined Spectroscopic (Infrared, Electronic, and X-ray Absorption) and DFT Investigation of Matrix-Isolated Iron, Cobalt, Nickel, and Zinc Dibromides.

The interactions of FeBr2, CoBr2, NiBr2, and ZnBr2 with Ne, Ar, Kr, Xe, CH4, and N2 matrices have been investigated using IR, electronic absorption, and X-ray absorption spectroscopies as well as DFT calculations. ZnBr2 is linear in all of the matrices. NiBr2 is linear in all but N2 matrices, where it is severely bent. For FeBr2 and CoBr2 there is a more gradual change, with evidence of nonlinearity in Xe and CH4 matrices as well as N2. In the N2 matrices, the presence of νNN modes blue-shifted from the "free" N2 values indicates the presence of physisorbed species, and the magnitude of the blue shift correlates with the shift in the ν3 mode of the metal dibromide. In the case of NiCl2 and NiBr2, chemisorbed species are formed after photolysis, but only if deposition takes place below 10 K. There was no evidence for chemisorbed species for NiF2 and FeBr2, and in the case of CoBr2 the evidence was not strong.

A Matrix Isolation and Computational Study of Molecular Palladium Fluorides: Does PdF6 Exist?

Palladium atoms generated by thermal evaporation and laser ablation were reacted with and trapped in F2/Ar, F2/Ne, and neat F2 matrices. The products were characterized by electronic absorption and infrared spectroscopy, together with relativistic density functional theory calculations as well as coupled cluster calculations. Vibrational modes at 540 and 617 cm(-1) in argon matrices were assigned to molecular PdF and PdF2, and a band at 692 cm(-1) was assigned to molecular PdF4. A band at 624 cm(-1) can be assigned to either PdF3 or PdF6, with the former preferred from experimental considerations. Although calculations might support the latter assignment, our conclusion is that in these detailed experiments there is no convincing evidence for PdF6.

Modelling the circularly and linearly polarised spectrum of [Ni(en)3]2+.

The relative intensity and band shapes of the low energy spin-allowed transitions in the linearly polarised and circular dichroism spectrum of [Ni(en)(3)](2+) have been calculated using a time-dependent density functional theory approach. The effect of the trigonal ligand-field is minimal and no splitting of the bands is predicted by the simulations or observed experimentally. The 'd-d' transitions of the [Ni(en)(3)](2+) ion are electric dipole allowed but gain much of their intensity through Herzberg-Teller vibronic coupling. Its CD spectrum is dominated by the low energy band, which gains its rotatory strength through the magnetic dipole-allowed character of the parent octahedral transition and the electric dipole character due to the trigonal field. The simulation of the spectrum incorporates the contribution from all inducing vibrational modes with significant involvement of the {NiN(6)} unit. Vibrations which are centred on the chelate rings are not important in generating intensity, reflecting the localised d-d' character of the transitions. Simulated linearly polarised and circular dichroism spectra of such an open-shell system are presented for the first time and predict the essential elements of the experimental spectra.

Modeling the interactions between polyoxometalates and their environment.

To develop a force field suitable both for polyoxometalates (POMs) and organic cations, the Merck molecular force field 94x (MMFF94x) has been selected to describe the counterions used in POMs synthesis and has been combined with our force field optimized for type-II POMs with electrostatic and Van der Waals interactions included in the potential. Nontransferability of force fields is well-known and, to overcome this limitation, a charge-scaling factor (SF) has been introduced and optimized to tune the POMs force field parameters and adapt them to MMFF94x. The mixed MMFF94x/POMFF-II force field has been optimized and tested on different clusters based on hepta-molybdate. To validate our mixed force field comparison of the results obtained after molecular mechanics (MM), geometry optimizations with density-functional (DFT) calculations have been performed on the smallest system of interest. This has enabled a study of the accuracy of different functionals, especially on the description of hydrogen bonding, to be made. Results are promising in terms of structural accuracy. MM geometry optimization can be used on small POM clusters, competing reasonably well with DFT. When quantum approaches increase considerably the computational cost because of the size of the system studied, MM can be used, with the small reservation that even if the charge SF introduced improves the performance of the force field, further optimizations of the nonbonded term and the model used for the atomic charges may be necessary in further studies.

Optimization of a molecular mechanics force field for type-II polyoxometalates focussing on electrostatic interactions: a case study.

In this study, we have focussed on type-II polyanions such as [M(7)O(24)](6-), and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type-I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed-charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4-interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM-optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta-anions interacting with organic molecules.

Optimization of a molecular mechanics force field for polyoxometalates based on a genetic algorithm.

A stochastic technique based on genetic algorithms was implemented to develop new force fields by optimizing molecular mechanics (MM) parameters. These force fields have been optimized for inorganic compounds such as polyoxometalates (POMs) and especially for type-I polymolybdate and polytungstate clusters. Focussing on the methodology of the development of the force fields, they were tested for the prediction of structural parameters, comparing the MM optimized structures with the geometry obtained after an optimization based on density functional theory. Results show that the genetic algorithm converges toward an optimum combination of parameters which successfully reproduces POMs structures with a high degree of accuracy.

Structural and vibrational study of [Mo7O24]6- and [W7O24]6-.

Density functional methods have been used to investigate the structure and the vibrational modes of [M7O24]6- isopolyanions of molybdenum and tungsten. Relativistic effects have been considered through the zeroth-order regular approximation (ZORA) and interactions with an aqueous environment modeled by the COSMO approach. A structural study of the two compounds has been performed, and the geometrical parameters obtained are in good agreement with experimental data. However, when the solvent is introduced in the model, deviations are found, especially for some tungsten-oxygen bonds which involve pseudoterminal oxygens. Thus, different computational strategies have been tested to reject any reliance on the COSMO model and the optimization algorithms. The variations compared to solid-state bond lengths appear to be due to the solvent. Infrared and Raman spectra have been also calculated in the gas phase and in water leading, for the first time, to a detailed assignment of the vibrational frequencies. The vibrational contributions of the aminopyridinium counterion [C5H7N2]+ have been isolated, improving the assignment of experimental spectra. Inclusion of solvent causes a shift toward lower frequencies and an increase in the intensity of the peaks. Spectra obtained using pseudo-gas-phase calculations reproduce the experimental data most satisfactorily, especially when the experiments are performed on the solid state.

Mercury-fluorine interactions: a matrix isolation investigation of Hg...F2, HgF2 and HgF4 in argon matrices.

HgF(2) and Hg have been trapped in dilute F(2)/Ar and neat F(2) matrices, subjected to UV-Vis and vac-UV photolysis and annealing, with the products identified by FTIR, UV-Vis-NIR and Hg L(3)-edge XAFS spectroscopic techniques. Whilst there was no convincing evidence for the formation of HgF(4) under our argon matrix isolation conditions, a new Hg...F(2) complex was identified and subsequent photolysis yielded HgF(2) very cleanly. Hg L(3)-edge EXAFS has provided the first experimental value of 1.94(2) A for the Hg-F bond length in HgF(2), which is in excellent agreement with the computational values incorporating relativistic effects.

Modeling the vibronic spectra of transition metal complexes: the ligand-field spectrum of [PtCl4]2-.

A framework for calculating the intensity distribution and vibrational fine structure in the polarized ligand-field spectrum of transition metal complexes using the Herzberg-Teller approach is introduced and used to model the spectrum of the [PtCl4]2- ion. The model uses geometries, vibrational frequencies, and transition moments generated using density functional calculations on the ground and excited states, which arise from spin-allowed reorganization of the d electrons. The model predicts the whole spectral trace, including the polarization, the difference in the frequency of the electronic origin, the band maximum and the vertical transition energy, and the temperature dependence of the band intensities and the frequencies of the band maxima. Excitation to the 1A2g state is accompanied by a vibrational progression in the breathing mode of the excited state, as observed experimentally. Excitation to both the 1B1g and 1Eg states is accompanied by a loss of planarity and extended vibrational progressions in two modes, and the resulting spectra are inherently of low resolution.

On the origin of paramagnetism in planar nickel(II) complexes.

The general rule that in Ni(II) d(8) chemistry, tetrahedral (or nearly tetrahedral) complexes have temperature dependent magnetic moments which are usually larger than the spin-only value whilst square planar complexes are diamagnetic is broken for certain Ni[P((t)Bu)(2)(O)NR](2) complexes. These have planar coordination for various alkyl groups but have the spectral and paramagnetic properties normally associated with tetrahedral systems. In contract to previous studies, density functional calculations show the unusual adoption of a high-spin rather than low-spin arrangement in the planar systems is due to the strong pi bonding of the amide group and the preference for a planar coordination is due to greater separation between the bulky nitrogen and phosphorus substituents.

Probing key coordination interactions: configurationally restricted metal activated CXCR4 antagonists.

The syntheses of configurationally restricted mono- and bis-macrocyclic copper(II) perchlorate complexes (copper(II) 5-benzyl-1,5,8,12-tetraazabicyclo[10.2.2]hexadecane and dicopper(II) 5,5'-[1,4-phenylenebis(methylene)]-bis(1,5,8,12-tetraazabicyclo[10.2.2]hexadecane)) are reported and the X-ray structure of the copper(II) mono-macrocyclic complex has been determined. EXAFS studies on the bis-macrocyclic species in aqueous solution show that the copper coordination spheres are essentially identical to the solid state structure, and do not vary in the presence of 20 equivalents of sodium acetate per metal centre. DFT calculations were carried out at the BP86/TZP level to determine the nature of potential binding interactions with CXCR4 aspartate residues. The alkylated single macrocyclic compound was modelled with an acetate included to represent the aspartate residue, demonstrating that the predicted macrocycle configuration has the lowest energy and the acetate interaction is effectively monodentate giving a distorted trigonal bipyramidal geometry at the copper centre. In vitro anti-HIV infection assays show that the configurationally restricted dicopper(II) complex is more active (average EC(50) = 0.026 microM against HIV-1) than the non-constrained dicopper(II) 1,1'-[1,4-phenylenebis(methylene)]-bis(1,4,8,11-tetraazacyclotetradecane) (average EC(50) = 0.047 microM against HIV-1) although it is an order of magnitude less active than the configurationally restricted dizinc(II) complex.

Computational study of solvent effects and the vibrational spectra of Anderson polyoxometalates.

The structures and vibrational frequencies of the type II Anderson heteropolyanions [TeMo6O24]6- and [IMo6O24]5- have been calculated by using density functional theory using a number of common functionals and basis sets. For the first time, Raman intensities have been calculated and the effect of solvent on the modeling has been investigated. The calculated IR and Raman spectral traces are in good agreement with experiment allowing the characteristic group frequencies for this class of polyoxometalate to be identified. The stretching vibrations of the molybdenum-oxygen bonds are predicted to occur at somewhat lower frequencies than in the type I polyoxometalates. Stretching of the heteroatom-oxygen bonds occurs at significantly lower frequencies than in the Keggin anions as a simple consequence of the higher coordination number of the central heteroatom in the Anderson systems. For the [Mo2O7]2- and [Mo6O19]2- ions, the relatively low negative charge leads to small structural changes when solvent is included. In these systems, solvent leads to an increase in the bond polarity and a decrease in the covalent bond orders, resulting in decreases in the calculated frequencies. For the Anderson anions, the higher negative charges leads to greater solvent effects with contraction of the clusters and increases in the frequencies of bands due to stretching of the two, cis-related molybdenum-oxygen bonds.

Bond orders between molecular fragments.

An extension of the Mayer bond order for the interaction between molecular fragments is presented. This approach allows the classical chemical concepts of bond order and valence to be utilised for fragments and the interactions between the fragments and symmetry-adapted linear combinations to be analysed. For high-symmetry systems, the approach allows the contribution from each irreducible representation to be assessed and provides a semiquantitative measure of the role of each bonding mode to interfragment interactions. The utility of this tool has been examined by a study of the bonding in symmetrical sandwich complexes. The validity of the frontier-orbital approach and the contributions from each frontier-orbital interaction can also be assessed within this model. As demonstrated by a study of a number of mixed-sandwich complexes, the model proves to be especially useful for low-symmetry systems in which separation of the sigma, pi and delta roles in bonding of the ligand is difficult to assess. The fragment bond order describes the interaction between preoptimized fragment orbitals and is independent of the charges that are placed on these fragments. Although the method allows the chemist to define fragments in any way they choose, most insight is gained by using the same frontier orbitals employed so successfully in perturbational molecular-orbital approaches. The results are free from the influence of the electron-counting method used to describe fragments, such as the rings and metals in sandwich complexes.

A crystallographic, EPR and theoretical study of the Jahn-Teller distortion in [CuTp2] (Tp- = tris[pyrazol-1-yl]hydridoborate).

Crystals of the title compound (1) contain two independent, centrosymmetric half-molecules per asymmetric unit. While both of these show Jahn-Teller elongated six-coordinate geometries, the lengths of the elongated Cu-N bonds in the two molecules differ by 0.117(2) A at 30 K. The structure of one of these molecules (molecule A) does not vary with temperature below 350 K. The other molecule (molecule B) shows Cu-N bond lengths that are temperature-dependent between 225 and 375 K, but do not vary further at lower temperature. This indicates a fluxional axis of Jahn-Teller elongation in this molecule at these higher temperatures. Consideration of the thermal parameters in these structures implies that the fluxionality in molecule B is frozen out near 150 K. This conclusion is supported by a Q-band powder EPR study. The d-d transition energies of molecules A and B have been calculated by several density function (DF) methods, including a time-dependent DF calculation. The crystallographic data have been reproduced using the vibronic coupling model of Burgi and Hitchman. This has shown that the different fluxionality regimes for molecules A and B are not a consequence of their different static molecular structures, but rather reflect their different local environments in the crystal.

Rigidity extremes in coordination chemistry: a fine energetic balance in the isolation of a trapped ligand inversion intermediate.

An unusual copper(ii) complex of a highly rigid and bulky ligand (a macrocycle-glyoxal condensate) has been synthesized and investigated via DFT calculations and structural characterisation.

Computational study of the vibrational spectra of alpha- and beta-Keggin polyoxometalates.

The structures and vibrational frequencies of the alpha- and beta-isomers of the phosphomolybdate Keggin anion [PMo(12)O(40)](3-) have been calculated by using density functional theory. Good agreement between the calculated unscaled vibrational frequencies and those determined experimentally and between the calculated and observed IR traces has been obtained allowing the IR and Raman spectra to be assigned. For the alpha-isomer, the agreement with experiment using the current level of theory is superior to that obtained previously. For the beta-isomer, for which no non-empirical study has previously been reported, the agreement with experiment is slightly poorer but still allows the spectrum to be assigned unambiguously. To calculate the structure and vibrational spectra of these large molydate cluster ions requires large basis sets and a good treatment of electron correlation and relativistic effects. For the 53-atom [PMo(12)O(40)](3-) ions, the computational demands are very high, requiring several months computational time. The calculated IR spectral traces for the two isomers are quite similar due to the relative flexibility of the molybdates, where the slight weakening of the bonding of the rotated trimetallic unit to the rest of the cluster in the beta-isomer is compensated by contraction of the bonds within the unit, and the structure of the [MO(6)] and [PO(4)] units in the two isomers is nearly identical. The vibrations characteristic of the bridging Mo-O-Mo bonds involve both the "2-2" junctions between rotated [M(3)O(13)] units and the "1-2" junctions between rotated and unrotated units. The separation of "ligand" and "interligand" vibrations is not clear. The vibrational analyses confirm the high symmetry, namely T(d) and C(3v) for the alpha- and beta-isomers, respectively, assumed by previous workers in this field. The characteristic group frequencies for the Type I polyoxometalates containing both edge- and corner-sharing I octahedra have been identified.

Computational investigation of the vibrational and electronic states of S2N2.

The structures and vibrational frequencies of the ground and excited states of S(2)N(2) have been calculated using density functional (DF) methods. Time-dependent DF theory (TDDFT) has been used to calculate the excitation energies of the lowest 20 singlet-singlet transitions using a variety of methods. All computational methods predict a small highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap. There is some disagreement in the ordering of the b(2g) and b(3g) pi orbitals. This is reflected in the ordering of the B(2u) and B(3u) states from the TDDFT calculations. The excitation energies and oscillator strengths strongly suggest it is the transitions to these states that are responsible for the experimental electronic spectrum. The calculated geometries and vibrational frequencies for these two states show that both have C(2v) equilibrium structures. Modelling of the vibrational progressions and band shapes suggest that the ordering of the states is B(2u)

Towards an understanding of the bonding in polyoxometalates through bond order and bond energy analysis.

The molecular and electronic structures of transition metal complexes, [MOCl5]n- (n = 2 for M = V,Nb,Ta and n = 1 for Mo,W) and mixed-metal polyoxometalates, [M'M5O19]3-V,Nb,Ta, M = Mo,W) containing a single terminal oxo group on each metal, and of complexes of the uranyl ion [UO2]2+, [UO2(H2O)5]2+ and [UO2Cl4]2-, have been calculated using density functional methods. The calculated structures of the complexes are in good agreement with available experimental parameters. For the mixed-metal hexametalates, for which no crystallographic data is available, the calculations predict a small tetragonal compression of the clusters with only minor structural changes compared to the parent molybdate and tungstate. The metal oxygen bonding in these anions has been probed using Mayer-Mulliken, bond energy and atoms in molecule analyses (AIM). These methods provide a consistent description of the bonding in polyoxometalates. The terminal bonds between transition metal or uranium and oxygen atoms have large sigma and pi components with the pi contributions exceeding the sigma bonding. The transition metals utilize their d orbitals almost exclusively to bond to oxygen whilst uranium uses both its 5f and 6d orbitals. Oxygen atom charges increase and covalency indexes decrease with coordination number, with a marked separation of these terms according to the oxygen atom type. The total valency and AIM energies of the oxygen atoms are predicted to be almost constant for all types of oxygen site. The constancy of the bonding power of the oxygen atoms appears to be an important factor in determining the gross structures and details of the bonding in polyoxometalates. The Mayer Mulliken approach provides direct characterization of the bonding power of atoms and the extent of the interaction between pairs of atoms that is consistent with the results of the considerably more computationally demanding bond energy and AIM approaches.

Electronic structure of the alpha and beta isomers of [Mo(8)O(26)](4-).

The structure and bonding in alpha and beta octamolybdate anions have been investigated using density functional methods. In general, good computational-experimental agreement for the geometrical parameters has been obtained. The electronic structure of the anions has been probed with molecular orbital and Mulliken-Mayer methods. All Mo-O interactions have been found to be predominantly d(Mo)-p(O) in character. Several multicentered molecular orbitals can be described as sigma or pi closed-loop structures, but the proposed connection with the stability of the polyanions is not completely supported by the calculations. Mayer indexes correspond to fractional multiple character for terminal bonds and approximately single or low-order character for bridging bonds, in accordance with structural and bond valence results. The valency analysis has yielded similar overall bonding capacity for the various oxygen atoms. A distribution of the negative charge over all types of oxygen sites and metal charges considerably smaller than the formal oxidation states have been obtained from the Mulliken analysis.