Recent advances in understanding blue copper proteins

The type 1 (T1) or blue Cu (BC) proteins are a highly studied group of electron transfer (ET) active sites in bioinorganic chemistry. In this review, we cover several more recent results which extend the understanding of the geometric and electronic structure of these interesting Cu ET sites. Spectroscopic methods in tandem with density functional theory (DFT) and time dependent-DFT (TD-DFT) calculations have been used in studies of S → Se variants as well as a series of metal-varied model complexes (M = Mn²⁺ → Zn²⁺). The ligand and metal perturbations further defined the origins of the unique spectral features of BC proteins. These unique spectral features show different temperature dependencies in different T1 sites, and contrasts drawn between their behaviors define the role of the protein in tuning the geometric and electronic structure of the BC site for function. This has been termed the ‘entatic’ or ‘rack-induced’ state in bioinorganic chemistry.     

用第一原理理解与预测巯基金纳米簇

This is an exciting time for studying thiolated gold nanoclusters.Single crystal structures of Au102(SR)44 and Au25(SR) 1-8 (—SR being an organothiolate group) bring both surprises and excitement in this field.First principles density functional theory (DFT) simulations turn out to be an important tool to understand and predict thiolated gold nanoclusters.In this review,I summarize the progresses made by us and others in applying first principles DFT to thiolated gold nanoclusters,as inspired by the recent ...     

Anion⋅⋅⋅Si Interactions in an Inverse Sandwich Complex: A Computational Study

Combination of an electron‐rich molecule (e.g. chloride anion or nitrile group) with a chlorinated cyclohexasilane ring produces a supramolecular inverse sandwich complex formed by two guests (Cl^? or R?C≡N) strongly bonded to both faces of a planar host (Si₆ ring). In‐depth theoretical studies were carried out to investigate the nature of the bonding interactions that generate such a stable complex. Second‐order Møller–Plesset perturbation theory (MP2) calculations confirmed that the presence of the Cl substituents is fundamental to the stability of the supramolecular assemblies. The density functional theory (DFT) functional wB97XD gave an estimation of the contribution of dispersion interactions to the binding energy. These interactions become more important as the Cl atoms of the rings are systematically replaced by methyl groups or hydrogen atoms. Analysis of the topology of the electron density and the reduced density gradient gave insight into the binding of the studied supramolecular assemblies.     

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.     

Design of Bioinorganic Materials at the Interface of Coordination and Biosupramolecular Chemistry

Protein assemblies have recently become known as potential molecular scaffolds for applications in materials science and bio‐nanotechnology. Efforts to design protein assemblies for construction of protein‐based hybrid materials with metal ions, metal complexes, nanomaterials and proteins now represent a growing field with a common aim of providing novel functions and mimicking natural functions. However, the important roles of protein assemblies in coordination and biosupramolecular chemistry have not been systematically investigated and characterized. In this personal account, we focus on our recent progress in rational design of protein assemblies using bioinorganic chemistry for (1) exploration of unnatural reactions, (2) construction of functional protein architectures, and (3) in vivo applications.     

Evidences for Chelating Complexes of Lithium with Phenylphosphinic and Phenylphosphonic Acids: A Spectroscopic and DFT Study

Abstract

Lithium complexes were prepared with phenylphosphinic and phenylphosphonic acids. The complexes were studied in the solid state using Fourier transform infrared spectroscopy spectroscopy and in solution (methanol) using ¹H, ¹³C, and ³¹P Nuclear magnetic resonance spectroscopy (NMR) spectroscopy; the most preferred structures of the complexes were determined by density functional theory (DFT) computational method. Although methanol has a strong solvation effect on lithium ions and ligands, which causes dissociation of the complexes, significant changes of the NMR spectra of the complexes (relative to those of the free ligands) were observed. The new spectroscopic results indicate the presence of the phenylphosphinic acid tautomer (I: C₆H₅PH(?O)OH) rather than that of phenyl-phosphorous acid (II: C₆H₅P(OH)₂) in deuterated methanol showing PH/PD exchange. On the other hand, tautomer I predominates in the complex with lithium without showing PH/PD exchange. The DFT calculations predict that tautomer I is the preferred structure in the case of free ligand and lithium complex. The absence of a PH/PD exchange in the complex is due to the formation of a chelating complex, rather than of a simple salt between lithium ion and the two oxygen atoms of I, which prevent tautomerization of I into II. DFT calculations support the formation of lithium chelating complexes. The lithium ion was found to affect the spectroscopic properties of phenylphosphinic acid more dramatically than those of phenylphosphonic acid.     

Correlation potentials for the He atom and the hydrogen molecule: A comparison between the correlation factor approach and DFT correlation energy functionals

Two points about correlation potentials have been dealt with in this article. The first one is related to the shape of some of the most representative correlation potentials applied to the ground state of the He atom. It is shown here that both LDA and two-body density correlation potentials compare well with that obtained through the quantum chemistry definition of correlation energy. This is an interesting result because, in previous works, it had been shown that none of the correlation potentials compared well with the Kohn–Sham one. The gradient-corrected correlation potentials exhibit a very different behavior to that of both exact potentials (quantum chemistry and Kohn–Sham ones). The other question posed here refers to how a reference to the two-body density must modify DFT functionals for the correlation energy, when a multideterminant wave function is needed. This question has been addressed by analyzing the variation of correlation potentials as the bond length of the H₂ molecule increases. The results show that an external reference to the two-body density qualitatively improves DFT correlation potentials and also that only those functionals explicitly depending on two-body density can give the quantitative correct trends. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 143–156, 1998     

A crystallographic and DFT study on a NHC complex of niobium oxide trifluoride

The complex [NbOF₃(Ipr)]₂, 1, was afforded in crystalline form by reaction of NbF₅ with the bulky NHC ligand 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) in toluene by slow contact with moisture air. The molecular structure of 1 was ascertained by X-ray diffraction, providing the first example of a dinuclear NbOF₃ derivative and also a rare case of niobium compound with a monodentate NHC. A DFT investigation has shown that the Nb–C bond consists of a weak NHC to Nb σ donation, reinforced by an electrostatic contribution presumably favored by the presence of the ancillary fluoride ligands. The computed enthalpy for the dissociation of one Ipr from 1 is ca. 36 kcal mol^?1. The presence of bulky 2,6-diisopropylphenyl substituents on the carbene ligand has negligible influence on the Nb–C bond, as highlighted by DFT analyses on simplified models.     

Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences

Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local second‐order Møller–Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. This performance is achieved through a utilization of the pseudospectral approximation and several levels of parallelization. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition‐metal‐containing systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling. The article describes the historical and new features of Jaguar, such as improved parallelization of many modules, innovations in ab initio pKa prediction, and new semiempirical corrections for nondynamic correlation errors in DFT. Jaguar applications in drug discovery, materials science, force field parameterization, and other areas of computational research are reviewed. Timing benchmarks and other results obtained from the most recent Jaguar code are provided. The article concludes with a discussion of challenges and directions for future development of the program. © 2013 Wiley Periodicals, Inc.     

REVIEW: SPECTROSCOPIC STUDIES OF OXOVANADIUM COORDINATION COMPOUNDS

Abstract

In this review we present selected examples of our studies of oxovanadium(IV) and oxovanadium(V) complexes relevant for the bioinorganic chemistry of vanadium. Some of the investigated complexes are good models for different steps of vanadium metabolism or for a better understanding of the structural and electronic peculiarities of the coordination spheres of these oxocations in biomolecules. The investigated systems include ligands such as nucleotides, carbohydrates, phosphates, amino acids, oxine derivatives, porphine-like cores and other simple organic and inorganic ligands. All these complexes have been systematically investigated by means of vibrational (infrared and Raman) and electronic spectroscopy and, in some cases, also by thermal and electrochemical behavior. The potentialities and possibilities of the spectroscopic methodologies are illustrated and discussed and some general trends, useful for the structural characterization of these and similar systems, are emphasized.     

The SCC-DFTB method and its application to biological systems

The Self-consistent charge density functional tight-binding (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy expression. Here, we review in detail the application of SCC-DFTB to biological systems and several extensions of the original formalism. The biological systems discussed turn out to be a challenge for DFT due to the occurrence of weak binding forces and charge transfer problems, both of which are not properly described by recent DFT-GGA functionals. Possible solutions and alternative strategies are presented and the role of SCC-DFTB in a general quantum chemical approach to biological systems is discussed     

The exchange-correlation potential of DFT obtained from a semiempirically fine-tuned Hartree–Fock density for inhomogeneous electron liquids

The present authors have given an exact theory of the exchange-correlation potential V _xc (r) in terms of (i) the exact ground-state electron density n(r) and (ii) the idempotent Dirac density matrix γ(r,?r′) generated by the DFT one-body potential V(r), having n(r) as its diagonal element. Here, we display two approximate consequences: (a) a form of V _xc (r) generated by the semiempirically fine-tuned HF density of Cordero et al. (N.A. Cordero, N.H. March, and J.A. Alonso, Phys. Rev. A 75, 052502 (2007)) and (b) the exchange-only potential V _x (r) determined solely by the HF ground state density for the Be atom.     

Statistical–mechanical models with separable many-body interactions: especially partition functions and thermodynamic consequences

We start from a classical statistical–mechanical theory for the internal energy in terms of three- and four-body correlation functions g ₃ and g ₄ for homogeneous atomic liquids like argon, with assumed central pair interactions f(r_ij){\phi(r_{ij})} . The importance of constructing the partition function (pf) as spatial integrals over g ₃, g ₄ and f{\phi} is stressed, together with some basic thermodynamic consequences of such a pf. A second classical example taken for two-body interactions is the so-called one-component plasma in two dimensions, for a particular coupling strength treated by Alastuey and Jancovici (J Phys (France) 42:1, 1981) and by Fantoni and Tellez (J Stat Phys 133:449, 2008). Again thermodynamic consequences provide a particular focus. Then quantum–mechanical assemblies are treated, again with separable many-body interactions. The example chosen is that of an N-body inhomogeneous extended system generated by a one-body potential energy V(r). The focus here is on the diagonal element of the canonical density matrix: the so-called Slater sum S(r, β), related to the pf by pf(b) = òS(r, b)d[(r)\vec]{{\rm pf}(\beta) = \int {S({\bf r}, \beta)}d\vec {r}}, β = (k _B T)⁻¹. The Slater sum S(r, β) can be related exactly, via a partial differential equation, to the one-body potential V(r), for specific choices of V which are cited. The work of Green (J Chem Phys 18:1123, 1950), is referred to for a generalization, but now perturbative, to two-body forces. Finally, to avoid perturbation series, the work concludes with some proposals to allow the treatment of extended assemblies in which regions of long-range ordered magnetism exist in the phase diagram. One of us (Z.D.Z.) has recently proposed a putative pf for a three-dimensional (3D) Ising model, based on two, as yet unproved, conjectures and has pointed out some important thermodynamic consequences of this pf. It would obviously be of considerable interest if such a pf, together with conjectures, could be rigorously proved.     

Evaluation of <S2> in density functional theory

The evaluation of in density functional theory (DFT) is considered. Wang et al. [J. Chem. Phys. 102, 3477 (1995)] have derived an approximate, local density expression for and in the present study their formula is evaluated using densities from unrestricted Hartree-Fock (UHF) and a range of DFT exchange-correlation functionals. The results are compared with those obtained by evaluating the conventional UHF expression using the Kohn-Sham orbitals, which is appropriate for the noninteracting system. A generalized gradient approximation for is then proposed and investigated.     

Metal-mediated Discrete Supramolecular Assemblies of Porphyrins

There is substantial recent interest worldwide in the construction of multiporphyrin assemblies which can either mimic naturally occurring multichromophore aggregates, such as the photosynthetic reaction center and the light harvesting complex of purple bacteria, or which can be used as electron- and/or energy-transfer molecular devices for advanced technological tasks. The metal-mediated self-assembly approach, which exploits the formation of coordination bonds between peripheral basic site(s) on the porphyrins and metal centers, has recently allowed the design and preparation of sophisticated supramolecular architectures whose complexity and function begin to approach the properties of naturally occurring systems. Within this framework, meso -pyridyl/phenyl porphyrins (PyPs), or strictly related chromophores, can provide geometrically well-defined connections to as many as four metal centers by coordination of the pyridyl groups. Several discrete assemblies of various nuclearities, in which the pyridylporphyrins are linkers binding metalloporphyrins and/or coordination compounds, have been constructed in recent years. Our contribution to this field is reviewed, with the aim of providing insight into the design of new, more elaborated architectures of higher order.     

Experimental and theoretical characterization of Fe<Subscript>2</Subscript>Cr trinuclear-oxo-centered complex with a CF<Subscript>2</Subscript>ClCOO<Superscript>–</Superscript> bridge

In this work, an atrinuclear-oxo-centered complex of the CrFe₂ type with the CF₂ClCOO^– bridging ligand is newly synthesized. The complex is characterized by experimental and theoretical methods. The optimized geometry and theoretical vibrational frequencies are computed using the density functional theory (DFT) method. Also, the AIM analysis was applied to study changes in topological parameters such as the electron density at critical points of all the bonds of the complex. In the optimized geometry of the complex, three metal ions form a trigonal-planar structure with a μ₃-O atom in its center. Each of M³⁺ metal ions has an octahedral coordination environment of oxygen atoms. The DFT results are in agreement with the experimental ones, confirming the validity of the optimized geometry for the complex.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory

In this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. In systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (EET) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. It is shown that the recently proposed approximate scheme (J. Chem. Phys. 2007, 126, 134116) for coupled excitations within a subsystem approach to time-dependent DFT is capable of describing both effects in a consistent manner, and is efficient enough to study even the large assemblies of chromophores occurring in the light-harvesting complex 2 (LH2) of the purple bacterium Rhodopseudomonas acidophila. A way to extract phenomenological coupling constants as used in model calculations on EET rates is outlined. The resulting EET coupling constants and spectral properties are in reasonable agreement with the available reference data. Possible problems related to the effective exchange-correlation kernel are discussed.