Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Geometrical isomers of [TEAH][Co(L-Se)(2)]center dot xH(2)O: synthesis, structural, spectroscopic and computational studies

Trans-1, [HNEt3][Co-III(L-Se)(2)]center dot H2O and cis-1, [HNEt3][Co-III(L-Se)(2)]center dot 3H(2)O have been synthesized and characterized by single-crystal X-ray studies. The counter ion Et3NH+ plays a crucial role in the crystal packing leading to the formation of two distinctly different supramolecular assemblies in the two complexes. In trans-1, Co-bisphenolate units and triethylamine molecules are arranged in a linear fashion leading to a supramolecular columnar assembly along the crystallographic a-axis. In this assembly, triethylammonium ions are sandwiched between successive Co-bisphenolate units and act as gluing agents joining Co-bisphenolate units on either side through C-H center dot center dot center dot pi interactions. In sharp contrast to trans-1, Co-bisphenolate units and triethylammonium ions in cis-1 are arranged in a helical supramolecular assembly through similar C-H center dot center dot center dot pi interactions along the crystallographic b-axis. The Se center dot center dot center dot Se van der Waals interactions may be responsible for the predominant occurrence of the cis-isomer. The cyclic voltammetric studies showed quasi-reversible waves for the cobalt(III) -> cobalt(II) reductions with E-1/2 = 0.635 and 0.628 V vs. Ag/AgCl for cis-1 (at similar to 5 degrees C) and trans-1 (at similar to 25 degrees C), respectively. DFT calculations show that the trans-form is the thermodynamic product with higher stability than the cis-one, which is consistent with the variable temperature H-1 NMR studies

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C( 9)-H groups of adjacent molecules. In the liquid phase, the presence of C-(HO)-O-... bonded forms is revealed by both vibrational and NMR spectroscopy. A Delta H value of - 8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-(HO)-O-... contacts relative to the C(9)-(HO)-O-... ones.

Electronic properties of 4,4 ',5,5 '-tetramethyl-2,2 '-biphosphinine (tmbp) in the redox series fac-[Mn(Br)(CO)(3)(tmbp)], [Mn(CO)(3)(tmbp)](2), and [Mn(CO)(3)(tmbp)](-): crystallographic, spectroelectrochemical, and DFT computational study

Stepwise electrochemical reduction of the complex fac-[Mn(Br)(CO)(3)(tmbp)] (tmbp = 4,4',5,5'-tetramethyl-2,2'-biphosphinine) produces the dimer [Mn(CO)(3)(tmbp)](2) and the five-coordinate anion [Mn(CO)(3)(tmbp)](-). All three members of the redox series have been characterized by single-crystal X-ray diffraction. The crystallographic data provide valuable insight into the localization of the added electrons on the (carbonyl)manganese and tmbp centers. In particular, the formulation of the two-electron-reduced anion as [Mn-0(CO)(3)(tmbp(-))](-) also agrees with the analysis of its IR nu(CO) wavenumbers and with the results of density functional theoretical (DFT) MO calculations on this compound. The strongly delocalized pi-bonding in the anion stabilizes its five-coordinate geometry and results in the appearance of several mixed Mn-to-tmbp charge-transfer/IL(tmbp) transitions in the near-UV-vis spectral region. A thorough voltammetric and UV-vis/IR spectroelectrochemical study of the reduction path provided evidence for a direct formation of [Mn(CO)(3)(tmbp)](-) via a two-electron ECE mechanism involving the [Mn(CO)(3)(tmbp)](.) radical transient. At ambient temperature [Mn(CO)(3)(tmbp)](-) reacts rapidly with nonreduced fac-[Mn(Br)(CO)(3)(tmbp)] to produce [Mn(CO)(3)(tmbp)](2). Comparison with the analogous 2,2'-bipyridine complexes has revealed striking similarity in the bonding properties and reactivity, despite the stronger pi-acceptor character of the tmbp ligand.

Solvent-dependent modulation of metal–metal electronic interactions in a dinuclear cyanoruthenate complex: a detailed electrochemical, spectroscopic and computational study

The dinuclear complex [{Ru(CN)4}2(μ-bppz)]4− shows a strongly solvent-dependent metal–metal electronic interaction which allows the mixed-valence state to be switched from class 2 to class 3 by changing solvent from water to CH2Cl2. In CH2Cl2 the separation between the successive Ru(II)/Ru(III) redox couples is 350 mVand the IVCT band (from the UV/Vis/NIR spectroelectrochemistry) is characteristic of a borderline class II/III or class III mixed valence state. In water, the redox separation is only 110 mVand the much broader IVCT transition is characteristic of a class II mixed-valence state. This is consistent with the observation that raising and lowering the energy of the d(π) orbitals in CH2Cl2 or water, respectively, will decrease or increase the energy gap to the LUMO of the bppz bridging ligand, which provides the delocalisation pathway via electron-transfer. IR spectroelectrochemistry could only be carried out successfully in CH2Cl2 and revealed class III mixed-valence behaviour on the fast IR timescale. In contrast to this, time-resolved IR spectroscopy showed that the MLCTexcited state, which is formulated as RuIII(bppz˙−)RuII and can therefore be considered as a mixed-valence Ru(II)/Ru(III) complex with an intermediate bridging radical anion ligand, is localised on the IR timescale with spectroscopically distinct Ru(II) and Ru(III) termini. This is because the necessary electron-transfer via the bppz ligand is more difficult because of the additional electron on bppz˙− which raises the orbital through which electron exchange occurs in energy. DFT calculations reproduce the electronic spectra of the complex in all three Ru(II)/Ru(II), Ru(II)/Ru(III) and Ru(III)/Ru(III) calculations in both water and CH2Cl2 well as long as an explicit allowance is made for the presence of water molecules hydrogen-bonded to the cyanides in the model used. They also reproduce the excited-state IR spectra of both [Ru(CN)4(μ-bppz)]2– and [{Ru(CN)4}2(μ-bppz)]4− very well in both solvents. The reorganization of the water solvent shell indicates a possible dynamical reason for the longer life time of the triplet state in water compared to CH2Cl2.

Dinitrogen release from arylpentazole: A picosecond time-resolved infrared, spectroelectrochemical, and DFT computational study

p-(Dimethylamino)phenyl pentazole, DMAP-N5 (DMAP = Me2N−C6H4), was characterized by picosecond transient infrared spectroscopy and infrared spectroelectrochemistry. Femtosecond laser excitation at 310 or 330 nm produces the DMAP-N5 (S1) excited state, part of which returns to the ground state (τ = 82 ± 4 ps), while DMAP-N and DMAP-N3 (S0) are generated as double and single N2-loss photoproducts with η ≈ 0.14. The lifetime of DMAP-N5 (S1) is temperature and solvent dependent. [DMAP-N3]+ is produced from DMAP-N5 in a quasireversible, one-electron oxidation process (E1/2 = +0.67 V). Control experiments with DMAP-N3 support the findings. DFT B3LYP/6-311G** calculations were used to identify DMAP-N5 (S1), DMAP-N3 +, and DMAP-N in the infrared spectra. Both DMAP-N5 (S1) and [DMAP-N5]+ have a weakened N5 ring structure.

Bridge-localized HOMO-binding character of divinylanthracene-bridged dinuclear ruthenium carbonyl complexes: spectroscopic, spectroelectrochemical, and computational studies

The electronic properties of four divinylanthracene-bridged diruthenium carbonyl complexes [{RuCl(CO)(PMe3)3}2(μ[BOND]CH[DOUBLE BOND]CHArCH[DOUBLE BOND]CH)] (Ar=9,10-anthracene (1), 1,5-anthracene (2), 2,6-anthracene (3), 1,8-anthracene (4)) obtained by molecular spectroscopic methods (IR, UV/Vis/near-IR, and EPR spectroscopy) and DFT calculations are reported. IR spectroelectrochemical studies have revealed that these complexes are first oxidized at the noninnocent bridging ligand, which is in line with the very small ν(C[TRIPLE BOND]O) wavenumber shift that accompanies this process and also supported by DFT calculations. Because of poor conjugation in complex 1, except oxidized 1+, the electronic absorption spectra of complexes 2+, 3+, and 4+ all display the characteristic near-IR band envelopes that have been deconvoluted into three Gaussian sub-bands. Two of the sub-bands belong mainly to metal-to-ligand charge-transfer (MLCT) transitions according to results from time-dependent DFT calculations. EPR spectroscopy of chemically generated 1+–4+ proves largely ligand-centered spin density, again in accordance with IR spectra and DFT calculations results.

Memory-based Embodied Cognition: a computational architecture

At its most fundamental, cognition as displayed by biological agents (such as humans) may be said to consist of the manipulation and utilisation of memory. Recent discussions in the field of cognitive robotics have emphasised the role of embodiment and the necessity of a value or motivation for autonomous behaviour. This work proposes a computational architecture – the Memory-Based Cognitive (MBC) architecture – based upon these considerations for the autonomous development of control of a simple mobile robot. This novel architecture will permit the exploration of theoretical issues in cognitive robotics and animal cognition. Furthermore, the biological inspiration of the architecture is anticipated to result in a mobile robot controller which displays adaptive behaviour in unknown environments.

Morphology, biomass and nutrient status of fine roots of Scots pine (Pinus sylvestris) as influenced by seasonal fluctuations in soil moisture and soil solution chemistry

A field monitoring study was carried out to follow the changes of fine root morphology, biomass and nutrient status in relation to seasonal changes in soil solution chemistry and moisture regime in a mature Scots pine stand on acid soil. Seasonal and yearly fluctuations in soil moisture and soil solution chemistry have been observed. Changes in soil moisture accounted for some of the changes in the soil solution chemistry. The results showed that when natural acidification in the soil occurs with low pH (3.5-4.2) and high aluminium concentration in the soil solution (> 3-10 mg l(-1)), fine root longevity and distribution could be affected. However, fine root growth of Scots pine may not be negatively influenced by adverse soil chemical conditions if soil moisture is not a limiting factor for root growth. In contrast, dry soil conditions increase Scots pine susceptibility to soil acidification and this could significantly reduce fine root growth and increase root mortality. It is therefore important to study seasonal fluctuations of the environmental variables when investigating and modelling cause-effect relationships.

Short-term effects of manipulated increase in acid deposition on soil, soil solution chemistry and fine roots in Scots pine (Pinus sylvestris) stand on a podzol

A manipulated increase in acid deposition (15 kg S ha(-1)), carried out for three months in a mature Scots pine (Pinus sylvestris) stand on a podzol, acidified the soil and raised dissolved Al at concentrations above the critical level of 5 mg l(-1) previously determined in a controlled experiment with Scots pine seedlings. The induced soil acidification reduced tree fine root density and biomass significantly in the top 15 cm of soil in the field. The results suggested that the reduction in fine root growth was a response not simply to high Al in solution but to the depletion of exchangeable Ca and Mg in the organic layer, K deficiency, the increase in NH4:NO3 ratio in solution and the high proton input to the soil by the acid manipulation. The results from this study could not justify the hypothesis of Al-induced root damage under field conditions, at least not in the short term. However, the study suggests that a short exposure to soil acidity may affect the fine root growth of mature Scots pine.