Ligand field theory, Pauli shields and ultra-covalency in organometallic chemistry.

This paper explores the ligand field picture applied to organometallic compounds. Given the dearth of experimental data, the high-level ab initio ligand field theory (aiLFT) method is deployed as a surrogate for experiment and the necessary d orbital sequences and relative energies are obtained computationally. These are fitted to local cellular ligand field (CLF) σ, π and δ bonding parameters. Results are reported for planar [Cu(CR3)4]-, (R = F, H), octahedral M(CO)6n (M = Fe, Mn, Cr, V, Ti; n = +2, +1, 0, -1, -2), and the sandwich compounds M(Cp)2 (Cp = cyclopentadienyl, M = Fe, Ni, V), [Ni(Cp)2]2+ and Cr(C6H6)2. With respect to the aiLFT framework, these organometallic systems behave just like coordination complexes and most maintain the integrity of their formal dn configurations. Both [Cu(CR3)4]- compounds are formulated as low-spin d8 CuIII species and have normal ligand fields consistent with their planar geometries. The metal carbonyls reveal a new way of counting valence electrons which only requires the CLF d orbital energy level diagram to rationalise the 18-electron rule as well as its many exceptions. The bonding in sandwich compounds shows a remarkable variation. In ferrocene, Cp- behaves as a strong field ligand, comparable to [CN]- in [Fe(CN)6]4-. Fe(Cp)2 is low spin as is Cr(C6H6)2. Cp- in Fe(Cp)2 is a weak σ donor, strong π donor and weak δ acceptor while benzene in Cr(C6H6)2 is also a weak σ and strong π donor but is a much better δ acceptor. In contrast, Cp- is weak field in high spin, 20-electron Ni(Cp)2 but 'ultra-covalent' in [Ni(Cp)2]2+. The formal IV oxidation state is too high for the ligand set and the integrity of the d6 configuration is lost. Similarly, [V(CO)6]- and [Ti(CO)6]2- are ultra-covalent except now the formal metal oxidation states are too negative. Both mechanisms relate to the breaching of the metal's 3s23p6 'Pauli shield' and these ultra-covalent systems lie outside the ab initio ligand field regime. However, within the ligand field regime, the bonding in 'coordination complexes' and 'organometallic compounds' has the same conceptual footing and the nature of the local σ, π and δ interactions can be extracted from analysing the ligand field d orbitals.

Revisiting the Fundamental Nature of Metal-Ligand Bonding: An Impartial and Automated Fitting Procedure for Angular Overlap Model Parameters.

The properties and reactivities of transition metal complexes are often discussed in terms of Ligand Field Theory (LFT), and with ab initio LFT a direct connection to quantum chemical wavefunctions was recently established. The Angular Overlap Model (AOM) is a widely used, ligand-specific parameterization scheme of the ligand field splitting that has, however, been restricted by the availability and resolution of experimental data. Using ab initio LFT, we present here a generalised, symmetry-independent and automated fitting procedure for AOM parameters that is even applicable to formally underdetermined or experimentally inaccessible systems. This method allows quantitative evaluations of assumptions commonly made in AOM applications, for example, transferability or the relative magnitudes of AOM parameters, and the response of the ligand field to structural or electronic changes. A two-dimensional spectrochemical series of tetrahedral halido metalates ([MII X4 ]2- , M=Mn-Cu) served as a case study. A previously unknown linear relationship between the halide ligands' chemical hardness and their AOM parameters was found. The impartial and automated procedure for identifying AOM parameters introduced here can be used to systematically improve our understanding of ligand-metal interactions in coordination complexes.

Quantum Bio-Inorganic Chemistry (QBIC) Society Special Collection.

This Editorial by Guest Editors L. Rulísek, M. Gruden, M. Orio and QBIC Society President R. J. Deeth summarizes the Chemistry Europe Special Collection on quantum bioinorganic chemistry, published in collaboration with the Quantum Bioinorganic Chemistry (QBIC) Society. The Collection, which recognizes of the strides made in this area of research, spans several of our portfolio journals Chemistry-A European Journal, the European Journal of Inorganic Chemistry, ChemPlusChem, ChemBioChem, ChemPhysChem, and ChemistryOpen, includes outstanding work in the field by authors across the world and we hope you enjoy reading them!

A Computational Analysis of the Intrinsic Plasticity of Five-Coordinate Cu(II) Complexes and the Factors Leading to the Breakdown of the Orbital Directing Effect in Paddlewheel Secondary Building Units.

Quantum chemical calculations on model copper paddlewheel (CPW) complexes of general formula [Cu2 (µ2 -O2 CR)4 L2 ] establish two local coordination geometries at the metal centers depending on the balance between equatorial and axial ligand fields. When the equatorial field is stronger than the axial field (large ligand field asymmetry), d x 2 - y 2 dominates the stereochemical activity of the d9 shell resulting in a relatively rigid, "orbitally directed" planar or square pyramidal structure. However, if the axial field is significantly increased, or the equatorial field moderately weakened, a small ligand field asymmetry results and both d x 2 - y 2 and d z 2 are involved in the stereochemical activity. This results in a "plastic," distorted trigonal bipyramidal geometry where the former axial ligand moves into one of the original four equatorial positions. Linkers already used to synthesize zinc-dabco MOFs (dabco = 1,4-diazabicyclo[2.2.2]octane) are shown to generate plastic CPW secondary building unit analogs with potential implications for conferring breathing behavior for MOFs which would currently be assumed to be rigid. © 2019 Wiley Periodicals, Inc.

Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp)2 ]2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H3 bpp]3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp)2 ]2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF4 ]- or [PF6 ]- anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required.

Spin Crossover in a Hexaamineiron(II) Complex: Experimental Confirmation of a Computational Prediction.

Single crystal structural analysis of [FeII (tame)2 ]Cl2 ⋅MeOH (tame=1,1,1-tris(aminomethyl)ethane) as a function of temperature reveals a smooth crossover between a high temperature high-spin octahedral d6 state and a low temperature low-spin ground state without change of the symmetry of the crystal structure. The temperature at which the high and low spin states are present in equal proportions is T1/2 =140 K. Single crystal, variable-temperature optical spectroscopy of [FeII (tame)2 ]Cl2 ⋅MeOH is consistent with this change in electronic ground state. These experimental results confirm the spin activity predicted for [FeII (tame)2 ]2+ during its de novo artificial evolution design as a spin-crossover complex [Chem. Inf. MODEL: 2015, 55, 1844], offering the first experimental validation of a functional transition-metal complex predicted by such in silico molecular design methods. Additional quantum chemical calculations offer, together with the crystal structure analysis, insight into the role of spin-passive structural components. A thermodynamic analysis based on an Ising-like mean field model (Slichter-Drickammer approximation) provides estimates of the enthalpy, entropy and cooperativity of the crossover between the high and low spin states.

DFT Analysis of Spin Crossover in Mn(III) Complexes: Is a Two-Electron S = 2 to S = 0 Spin Transition Feasible?

Six-coordinate, rigorously octahedral d4 Mn(III) spin crossover (SCO) complexes are limited by symmetry to an S = 1 (intermediate spin, IS) to S = 2 (high spin, HS) transition. In order to realize the potential S = 0 to S = 2 transition, a lower symmetry and/or change in coordination number is needed, which we explore here computationally. First, a number of complexes are analyzed to develop a reliable and relatively fast DFT protocol for reproducing known Mn(III) spin state energetics. The hybrid meta-GGA functional TPSSh with a modest split valence plus polarization basis set and an empirical dispersion correction is found to predict correctly the ground spin state of Mn(III) complexes, including true low-spin (LS) S = 0 systems, with a range of donor sets including the hexadentate [N4O2] Schiff base ligands. The electronic structure design criteria necessary for realizing a ΔS = 2 SCO transition are described, and a number of model complexes are screened for potential SCO behavior. Five-coordinate trigonal-bipyramidal symmetry fails to yield any suitable systems. Seven-coordinate, approximately pentagonal bipyramidal symmetry is more favorable, and when a known pentadentate macrocyclic donor is combined with π-acceptor axial ligands, a novel Mn(III) complex, [Mn(PABODP)(PF3)2]3+ (PABODP = 2,13-dimethyl-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),2,12,14,16-pentaene), is predicted to have the right spin state energetics for an S = 0 to S = 2 transition. Successful synthesis of such a complex could provide the first example of a ΔS = 2 SCO transition for d4 Mn(III). However, the combination of a rigid macrocycle and a high coordination number dilutes the stereochemical activity of the d electrons, leading to relatively small structural changes between HS and LS systems. It may therefore remain a challenge to realize strong cooperative effects in Mn(III) systems.

A Unified Treatment of the Relationship Between Ligand Substituents and Spin State in a Family of Iron(II) Complexes.

The influence of ligands on the spin state of a metal ion is of central importance for bioinorganic chemistry, and the production of base-metal catalysts for synthesis applications. Complexes derived from [Fe(bpp)2 ](2+) (bpp=2,6-di{pyrazol-1-yl}pyridine) can be high-spin, low-spin, or spin-crossover (SCO) active depending on the ligand substituents. Plots of the SCO midpoint temperature (T1/2 ) in solution vs. the relevant Hammett parameter show that the low-spin state of the complex is stabilized by electron-withdrawing pyridyl ("X") substituents, but also by electron-donating pyrazolyl ("Y") substituents. Moreover, when a subset of complexes with halogeno X or Y substituents is considered, the two sets of compounds instead show identical trends of a small reduction in T1/2 for increasing substituent electronegativity. DFT calculations reproduce these disparate trends, which arise from competing influences of pyridyl and pyrazolyl ligand substituents on Fe-L σ and π bonding.

Integration of Ligand Field Molecular Mechanics in Tinker.

The ligand field molecular mechanics (LFMM) method for transition-metal complexes has been integrated in Tinker, an easily available and popular molecular modeling software package. The capability to calculate LFMM potentials has been provided by extending the functional forms of the Tinker package as well as by integrating routines for calculating the ligand field stabilization energy (LFSE), which is central to LFMM. The capabilities of the implementation are illustrated by both static calculations on the two spin states of [Fe(NH3)6](2+) and on [Cu(NH3)m](2+) (m = 4, 5, 6) and dynamic (LFMD) simulations of an FeN6-type spin-crossover compound. In addition to showing that results obtained with the Tinker-LFMM implementation are consistent with those of experiment and other computational methods and programs, we note that whereas LFMM is able to handle the conventional tetragonal Jahn-Teller distortion of the bond distances in [Cu(NH3)6](2+), the LFSE term is also necessary in order to obtain even qualitatively correct coordination geometries for the two lower-coordinate copper complexes.

Ring Closure To Form Metal Chelates in 3D Fragment-Based de Novo Design.

We describe a method for the design of multicyclic compounds from three-dimensional (3D) molecular fragments. The 3D building blocks are assembled in a controlled fashion, and closable chains of such fragments are identified. Next, the ring-closing conformations of such formally closable chains are identified, and the 3D model of a cyclic or multicyclic molecule is built. Embedding this method in an evolutionary algorithm results in a de novo design tool capable of altering the number and nature of cycles in species such as transition metal compounds with multidentate ligands in terms of, for example, ligand denticity, type and length of bridges, identity of bridgehead terms, and substitution pattern. An application of the method to the design of multidentate nitrogen-based ligands for Fe(II) spin-crossover (SCO) compounds is presented. The best candidates display multidentate skeletons new to the field of Fe(II) SCO yet resembling ligands deployed in other fields of chemistry, demonstrating the capability of the approach to explore structural variation and to suggest unexpected and realistic molecules, including structures with cycles not found in the building blocks.

Solid-state interconversions: unique 100 % reversible transformations between the ground and metastable states in single-crystals of a series of nickel(II) nitro complexes.

The solid-state, low-temperature linkage isomerism in a series of five square planar group 10 phosphino nitro complexes have been investigated by a combination of photocrystallographic experiments, Raman spectroscopy and computer modelling. The factors influencing the reversible solid-state interconversion between the nitro and nitrito structural isomers have also been investigated, providing insight into the dynamics of this process. The cis-[Ni(dcpe)(NO2)2] (1) and cis-[Ni(dppe)(NO2)2] (2) complexes show reversible 100 % interconversion between the η(1)-NO2 nitro isomer and the η(1)-ONO nitrito form when single-crystals are irradiated with 400 nm light at 100 K. Variable temperature photocrystallographic studies for these complexes established that the metastable nitrito isomer reverted to the ground-state nitro isomer at temperatures above 180 K. By comparison, the related trans complex [Ni(PCy3)2(NO2)2] (3) showed 82 % conversion under the same experimental conditions at 100 K. The level of conversion to the metastable nitrito isomers is further reduced when the nickel centre is replaced by palladium or platinum. Prolonged irradiation of the trans-[Pd(PCy3)2(NO2)2] (4) and trans-[Pt(PCy3)2(NO2)2] (5) with 400 nm light gives reversible conversions of 44 and 27 %, respectively, consistent with the slower kinetics associated with the heavier members of group 10. The mechanism of the interconversion has been investigated by theoretical calculations based on the model complex [Ni(dmpe)Cl(NO2)].

First principles calculation of a large variation in dielectric tensor through the spin crossover in the CsFe[Cr(CN)6] Prussian blue analogue.

The dielectric response of spin-crossover (SCO) materials is a key property facilitating their use in next-generation information processing technologies. Solid state hybrid density functional theory calculations show that the temperature-induced and strongly hysteretic SCO transition in the Cs(+)Fe(2+)[Cr(3+)(CN(-))6] Prussian blue analogue (PBA) is associated with a large change (Δ) in both the static, Δɛ(0)(HS - LS), and high frequency, Δɛ(∞)(HS - LS) dielectric constants. The SCO-induced variation in CsFe[Cr(CN)6] is significantly greater than the experimental Δɛ values observed previously in other SCO materials. The phonon contribution, Δɛ(phon)(HS - LS), determined within a lattice dynamics approach, dominates over the clamped nuclei term, Δɛ(∞)(HS - LS), and is in turn dominated by the low-frequency translational motions of Cs(+) cations within the cubic voids of the Fe[Cr(CN)6](-) framework. The Cs(+) translational modes couple strongly to the large unit cell volume change occurring through the SCO transition. PBAs and associated metal-organic frameworks emerge as a potentially fruitful class of materials in which to search for SCO transitions associated with large changes in dielectric response and other macroscopic properties.

Molecular modeling for Cu(II)-aminopolycarboxylate complexes: structures, conformational energies, and ligand binding affinities.

A ligand field molecular mechanics (LFMM) force field (FF) has been developed for d(9) copper(II) complexes of aminopolycarboxylate ligands. Training data were derived from density functional theory (DFT) geometry optimizations of 14 complexes comprising potentially hexadentate N2O4, tetrasubstituted ethylenediamine (ed), and propylenediamine cores with various combinations of acetate and propionate side arms. The FF was validated against 13 experimental structures from X-ray crystallography including hexadentate N2O4 donors where the nitrogens donors are forced to be cis and bis-tridentate ONO ligands which generate complexes with trans nitrogen donors. Stochastic conformational searches for [Cu{ed(acetate)n(propionate)(4-n)}](2-), n = 0-4, were carried out and the lowest conformers for each system reoptimized with DFT. In each case, both DFT and LFMM predict the same lowest-energy conformer and the structures and energies of the higher-energy conformers are also in satisfactory agreement. The relative interaction energies for n = 0, 2, and 4 computed by molecular mechanics correlate with the experimental log ß binding affinities. Adding in the predicted log ß values for n = 1 and 3 suggest for this set of complexes a monotonic decrease in log ß as the number of propionate arms increases.

Synthetic, crystallographic, and computational study of copper(II) complexes of ethylenediaminetetracarboxylate ligands.

Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands H(4)eda3p and H(4)eddadp (H(4)eda3p = ethylenediamine-N-acetic-N,N',N'-tri-3-propionic acid; H(4)eddadp = ethylenediamine-N,N'-diacetic-N,N'-di-3-propionic acid) have been prepared. An octahedral trans(O(6)) geometry (two propionate ligands coordinated in axial positions) has been established crystallographically for the Ba[Cu(eda3p)]·8H(2)O compound, while Ba[Cu(eddadp)]·8H(2)O is proposed to adopt a trans(O(5)) geometry (two axial acetates) on the basis of density functional theory calculations and comparisons of IR and UV-vis spectral data. Experimental and computed structural data correlating similar copper(II) chelate complexes have been used to better understand the isomerism and departure from regular octahedral geometry within the series. The in-plane O-Cu-N chelate angles show the smallest deviation from the ideal octahedral value of 90°, and hence the lowest strain, for the eddadp complex with two equatorial ß-propionate rings. A linear dependence between tetragonality and the number of five-membered rings has been established. A natural bonding orbital analysis of the series of complexes is also presented.

Structure and biosynthesis of scabichelin, a novel tris-hydroxamate siderophore produced by the plant pathogen Streptomyces scabies 87.22.

Scabichelin and turgichelin, novel tris-hydroxamate siderophores, were isolated from Streptomyces antibioticus NBRC 13838/Streptomyces scabies JCM 7914 and Streptomyces turgidiscabies JCM 10429, respectively. The planar structures of scabichelin and turgichelin were elucidated by mass spectrometry, and 1- and 2-D NMR spectroscopic analyses of their gallium(III) complexes. The relative and absolute stereochemistry of the metabolites was determined by the modified Marfey's method in conjunction with computational modelling and NOESY NMR analysis of Ga-scabichelin and Ga-turgichelin. Genome sequence analysis of the plant pathogen Streptomyces scabies 87.22 identified a gene cluster containing a gene encoding a nonribosomal peptide synthetase (NRPS) that was predicted to direct the production of a pentapeptide with structural similarities to scabichelin and turgichelin. Comparative LC-MS/MS analyses of iron-deficient culture supernatants from wild type S. scabies 87.22 and a mutant in which the NRPS gene had been disrupted, and scabichelin purified from S. antibioticus, showed that scabichelin is the metabolic product of the cryptic gene cluster, strongly suggesting that it functions as a siderophore.

Bipyrimidine ruthenium(II) arene complexes: structure, reactivity and cytotoxicity.

The synthesis and characterization of complexes [(η(6)-arene)Ru(N,N')X][PF(6)], where arene is para-cymene (p-cym), biphenyl (bip), ethyl benzoate (etb), hexamethylbenzene (hmb), indane (ind) or 1,2,3,4-tetrahydronaphthalene (thn), N,N' is 2,2'-bipyrimidine (bpm) and X is Cl, Br or I, are reported, including the X-ray crystal structures of [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)I][PF(6)] and [(η(6)-etb)Ru(bpm)Cl][PF(6)]. Complexes in which N,N' is 1,10-phenanthroline (phen), 1,10-phenanthroline-5,6-dione or 4,7-diphenyl-1,10-phenanthroline (bathophen) were studied for comparison. The Ru(II) arene complexes undergo ligand-exchange reactions in aqueous solution at 310 K; their half-lives for hydrolysis range from 14 to 715 min. Density functional theory calculations on [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-p-cym)Ru(bpm)Br][PF(6)], [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)Br][PF(6)] and [(η(6)-bip)Ru(bpm)I][PF(6)] suggest that aquation occurs via an associative pathway and that the reaction is thermodynamically favourable when the leaving ligand is I > Br ≈ Cl. pK (a)* values for the aqua adducts of the complexes range from 6.9 to 7.32. A binding preference for 9-ethylguanine (9-EtG) compared with 9-ethyladenine (9-EtA) was observed for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-hmb)Ru(bpm)Cl](+), [(η(6)-ind)Ru(bpm)Cl](+), [(η(6)-thn)Ru(bpm)Cl](+), [(η(6)-p-cym)Ru(phen)Cl](+) and [(η(6)-p-cym)Ru(bathophen)Cl](+) in aqueous solution at 310 K. The X-ray crystal structure of the guanine complex [(η(6)-p-cym)Ru(bpm)(9-EtG-N7)][PF(6)](2) shows multiple hydrogen bonding. Density functional theory calculations show that the 9-EtG adducts of all complexes are thermodynamically preferred compared with those of 9-EtA. However, the bmp complexes are inactive towards A2780 human ovarian cancer cells. Calf thymus DNA interactions for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)] and [(η(6)-p-cym)Ru(phen)Cl][PF(6)] consist of weak coordinative, intercalative and monofunctional coordination. Binding to biomolecules such as glutathione may play a role in deactivating the bpm complexes.

A computational approach to tuning the photochemistry of platinum(IV) anticancer agents.

Diazido Pt(IV) complexes are inert stable prodrugs that can be photoactivated to produce Pt(II) species with promising anticancer activity. Our studies of the photochemistry of Pt(IV) complexes, [Pt(X)(2) (Y)(2) (Z)(2) ](0/-1) (X=N-ligands (NH(3) , pyridine, etc.)/S(CH(3) )(2) /H(-) , Y=(pseudo)halogen (N(3) (-) , I(-) ), Z=OR(-) , R=H, Ac) by time-dependent density functional theory (TDDFT) show close agreement with spectroscopic data. Broad exploration of cis/trans geometries, trans influences, the nature of the OR(-) and (pseudo)halogen ligands, electron-withdrawing/donating/delocalising substituents on the N-ligands, and intramolecular H bonds shows that: 1) the design of platinum(IV) complexes with intense bands shifted towards longer wavelengths (from 289 to ∼330 nm) can be achieved by introducing intramolecular H bonds involving the OH ligands and 2-hydroxyquinoline or by iodido ligands; 2) mesomeric electron-withdrawing substituents on pyridine result in low-energy absorption with significant intensity in the visible region; and 3) the distinct makeup of the molecular orbitals involved in the electronic transitions for cis/trans-{Pt(N(3) )(2) } isomers results in different photoproducts. In general, the comparison of the optimised geometries shows that Pt(IV) complexes with longer PtL bonds are more likely to undergo photoreduction with longer-wavelength light. The novel complex trans,trans,trans-[Pt(N(3) )(2) (OH)(2) (NH(3) )(4-nitropyridine)] with predicted absorption in the visible region has been synthesised. The experimental UV/Vis spectrum in aqueous solution correlates well with the intense band in the computed spectrum, whereas the overlay in the low-energy region can be improved by a solvent model. This combined computational and experimental study shows that TDDFT can be used to tune the coordination environment for optimising photoactive Pt(IV) compounds as anticancer agents.

Combined theoretical and computational study of interstrand DNA guanine-guanine cross-linking by trans-[Pt(pyridine)2] derived from the photoactivated prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2].

Molecular modeling and extensive experimental studies are used to study DNA distortions induced by binding platinum(II)-containing fragments derived from cisplatin and a new class of photoactive platinum anticancer drugs. The major photoproduct of the novel platinum(IV) prodrug trans,trans,trans-[Pt(N(3))(2)(OH)(2)(py)(2)] (1) contains the trans-{Pt(py)(2)}(2+) moiety. Using a tailored DNA sequence, experimental studies establish the possibility of interstrand binding of trans-{Pt(py)(2)}(2+) (P) to guanine N7 positions on each DNA strand. Ligand field molecular mechanics (LFMM) parameters for Pt-guanine interactions are then derived and validated against a range of experimental structures from the Cambridge Structural Database, published quantum mechanics (QM)/molecular mechanics (MM) structures of model Pt-DNA systems and additional density-functional theory (DFT) studies. Ligand field molecular dynamics (LFMD) simulation protocols are developed and validated using experimentally characterized bifunctional DNA adducts involving both an intra- and an interstrand cross-link of cisplatin. We then turn to the interaction of P with the DNA duplex dodecamer, d(5'-C(1)C(2)T(3)C(4)T(5)C(6)G(7)T(8)C(9)T(10)C(11)C(12)-3')·d(5'-G(13)G(14)A(15)G(16)A(17)C(18)G(19)A(20)G(21)A(22)G(23)G(24)-3') which is known to form a monofunctional adduct with cis-{Pt(NH(3))(2)(py)}. P coordinated to G(7) and G(19) is simulated giving a predicted bend toward the minor groove. This is widened at one end of the platinated site and deepened at the opposite end, while the P-DNA complex exhibits a global bend of ∼67° and an unwinding of ∼20°. Such cross-links offer possibilities for specific protein-DNA interactions and suggest possible mechanisms to explain the high potency of this photoactivated complex.

An in silico design tool for Fe(II) spin crossover and light-induced excited spin state-trapped complexes.

The discovery of new coordination complexes that can support spin crossover (SCO) or light-induced excited spin state trapping (LIESST) could be radically improved by better computational tools. While methods such as density functional theory (DFT) are capable of high accuracy, they are too slow for molecular discovery, where millions of individual calculations may be required. In contrast, empirical ligand-field molecular mechanics (LFMM) captures the d-electron effects implicit in DFT and thus can be as accurate, but LFMM is up to 4 orders of magnitude faster. We demonstrate for simple Fe(II) am(m)ines how LFMM can be used to redesign "old" systems to generate novel, potential SCO and LIESST complexes.

Structural and mechanistic insights into the oxy form of tyrosinase from molecular dynamics simulations.

The first, long time scale (16-ns) ligand field molecular dynamics (LFMD) simulations of the oxy form of tyrosinase are reported. The calculations use our existing type 3 copper force field for the peroxido-bridged [Cu(2)O(2)](2+) unit which is here translated from MMFF into the AMBER format together with a new charge scheme. The protein secondary and tertiary structures are not significantly altered by removing the 'caddie' protein, ORF378, which must be bound to tyrosinase before crystals will grow. A comprehensive principal component analysis of the Cartesian coordinates from the final 8 ns shows that the protein backbone is relatively rigid. However, the significant butterfly fold of the [Cu(2)O(2)](2+) moiety observed in the X-ray structure, presumably due to the caddie protein tyrosine at the active site, is absent in the simulations. LFMD gives a clear and persistent distinction between equatorial and axial Cu-N distances, with the latter about 0.2 A longer and remaining syn to each other. However, the two coordination spheres display important differences. LFMD simulations of the symmetric model complex [mu-eta(2):mu(2)-O(2){Cu(Meim)(3)}(2)](2+) (Meim is 5-methyl-1H-imidazole) provide a mechanism for syn-anti interchange of axial ligands which suggests, in combination with the old experimental X-ray data, the new LFMD simulations and traditional coordination chemistry arguments, that His(54) on Cu(A) is 'insipiently axial' and that a combination of a butterfly distortion of the [Cu(2)O(2)](2+) group and a rotation of the Cu(A)(His)(3) moiety converts the vacant, initially axial, binding site on Cu(A) into a much more favourable equatorial site.