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Abhik Ghosh

Publications and source records attributed to Abhik Ghosh.

At least 19 recordsLinked to original sources
PubMed2006

When being straight bends rules: a rationale for the linear FeNO unit in the low-spin square-pyramidal {FeNO}7 tetracyanonitrosylferrate(2-) anion.

All low-spin S=1/2 heme-NO complexes feature FeNO angles of about 140 degrees . In contrast, the square-pyramidal [Fe(CN)(4)(NO)](2-) complex features an exactly linear {FeNO}(7) unit. We have sought here to determine a possible, simple molecular orbital (MO) rationale for these structural variations. A DFT-based (DFT=density functional theory) MO analysis shows that the linearity of the latter stems from the greater pyramidalization of the Fe center, relative to nitrosylheme, which results in significant differences in d orbital hybridization. Thus, the singly occupied molecular orbital (SOMO) of [Fe(CN)(4)(NO)](2-) , while primarily Fe dz2-based, also has a significant amount of 4p(z) character, which makes it less stereochemically active, accounting for the linearity of the FeNO unit.

Ferric Compounds↗
PubMed2006

Transition metal spin state energetics and noninnocent systems: challenges for DFT in the bioinorganic arena.

Although density functional theory (DFT) provides a generally good description of transition metal systems, we have identified several cases, involving Fe(III) porphyrins and related systems, where common functionals fail to correctly describe the energetics of the different low-lying spin states. The question of metal- versus ligand-centered oxidation in high-valent transition metal complexes is also a challenging one for DFT calculations, as I have tried to illustrate with examples from among porphyrin, corrole, biliverdine, and NO complexes. In a number of cases, I have compared results obtained with different exchange-correlation functionals; in addition, I have added a discussion on the relative performance of pure versus hybrid functionals. Finally, I have offered some thoughts on the role that traditional wavefunction-based ab initio methods, now essentially absent from the bioinorganic arena, might play in the future.

Chemistry, Bioinorganic↗
PubMed2006

Biliverdine-based metalloradicals: sterically enhanced noninnocence.

This is a first density functional theory survey of transition-metal biliverdines (Blv), where we have chosen to focus on key Mn, Fe, Co, and Cu complexes. According to the calculations, the complexes are invariably noninnocent, featuring Blv*2- ligand radicals. In this, biliverdine complexes resemble metallocorroles, but the parallels are only approximate. Briefly, metallobiliverdines exhibit a much greater tendency to adopt noninnocent electronic structures than analogous metallocorroles. The O...O nonbonded contacts in biliverdines apparently preclude the formation of short metal-N bonds that, in turn, could stabilize high-valent metal ions. Thus, while most copper corroles (Cor) exhibit diamagnetic CuIII ground states, copper biliverdines are clearly Cu(II)Blv*2- species. In the same spirit, while chloroiron corroles are best described as FeIII(S = 3/2)Cor*2-,the analogous biliverdine derivative seems best described as Fe(III)(S = 5/2)Blv*2-, i.e., featuring a high-spin FeIII center with long (>2.0 A) Fe-N bond distances. Overall, the results highlight the important role that steric effects may play in modulating the electronic structures and the potentially noninnocent nature of transition-metal complexes.

Biliverdine↗
PubMed2006

Theoretical evidence favoring true iron(V)-oxo corrole and corrolazine intermediates.

Although many formally FeV intermediates are known in the form of peroxidase compound I intermediates and their synthetic models, "true" d3 FeVO intermediates have remained elusive and hence a Holy Grail of sorts for many bioinorganic chemists. Very recently, Newcomb and co-workers provided transient absorption spectroscopic evidence suggestive of FeVO corrole intermediates. Here, we report DFT calculations predicting nearly isoenergetic FeVO and FeIVO corrolato2-* states for Fe(corrolato)(O) intermediates. In the course of a theoretical search for systems in which a true FeVO state might be favored by a clear and substantial margin of energy, we have identified corrolazine as a promising supporting ligand; thus, we find that with corrolazine, the FeVO states are favored by at least 0.5 eV over FeIVO corrolazinato2-* states.

Journal Article↗
PubMed2006

Iron(III)-nitro porphyrins: theoretical exploration of a unique class of reactive molecules.

DFT(PW91/TZP) calculations, including full geometry optimizations, have been carried on [FeII(P)(NO2)]-, Fe(III)(P)(NO2), [Fe(II)(P)(NO2)(py)]-, Fe(III)(P)(NO2)(py), [Fe(III)(P)(NO2)2]-, and Fe(III)(P)(NO2)(NO), where P is the unsubstituted porphine dianion, as well as on certain picket fence porphyrin (TPivPP) analogues. The bonding in [Fe(II)(P)(NO2)]- and Fe(III)(P)(NO2), as well as in their pyridine adducts, reveals a sigma-donor interaction of the nitrite HOMO and the Fe dz2 orbital, where the Fe-Nnitro axis is defined as the z direction and the nitrite plane is identified as xz. Both molecules also feature a pi-acceptor interaction of the nitrite LUMO and the Fe dyz orbital, whereas the SOMO of the Fe(III)-nitro complexes may be identified as dxz. The Fe(III)-nitro porphyrins studied all exhibit extremely high adiabatic electron affinities, ranging from about 2.5 eV for Fe(III)(P)(NO2) and Fe(III)(P)(NO2)(py) to about 3.4 eV for their TPivPP analogues. Transition-state optimizations for oxygen-atom transfer from Fe(III)(P)(NO2) and Fe(III)(P)(NO2)(py) to dimethyl sulfide yielded activation energies of 0.45 and 0.77 eV, respectively, which is qualitatively consistent with the observed far greater stability of Fe(III)(TPivPP)(NO2)(py) relative to Fe(III)(TPivPP)(NO2). Addition of NO to yield {FeNO}6 nitro-nitrosyl adducts such as Fe(P)(NO2)(NO) provides another mechanism whereby Fe(III)-nitro porphyrins can relieve their extreme electron affinities. In Fe(P)(NO2)(NO), the bonding involves substantial Fe-NO pi-bonding, but the nitrite acts essentially as a simple sigma-donor, which accounts for the relatively long Fe-Nnitro distance in this molecule.

Journal Article↗
PubMed2006

Electronic ménages a trois: a molecular orbital perspective of protonated ferryl intermediates and synthetic models.

Presented here is a molecular orbital perspective of various S=1 iron(IV)-hydroxo compound II intermediates as well as of synthetic heme and nonheme analogues. A key conceptual issue concerns how the iron(IV) center in these species coexists with highly reducing alkoxide, thiolate, phenolate, and hydroperoxide ligands. We suggest that a clue to this conundrum involves a three-way splitting of the spin density among the iron and two pi-basic ligands, which effectively delocalizes the high positive charge away from the iron.

Hemeproteins↗
PubMed2006

A DFT overview of high-valent iron, cobalt and nickel tetraamidomacrocyclic ligand (TAML) complexes: the end of innocence?

Amidato-N ligands are normally viewed as classic, strongly sigma-donating, innocent ligands. However, when coordinated to high-valent transition metal centers, tetraamidomacrocyclic ligands are often substantially non-innocent, i.e., exhibit radical character involving the amido pi-systems. Even the so-called MAC* ligand, generally considered to be an innocent ligand, is non-innocent in several of its known complexes.

Cobalt↗
PubMed2006

Trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, and selenido complexes. An electronic-structural overview.

Using density functional theory calculations, we have carried out a broad survey of trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, selenido, and hydroxo complexes, with tripodal tetradentate "triureidoamine" supporting ligands. The calculations reproduce the experimentally observed high-spin states of these compounds; a multifunctional analysis suggests that the high-spin nature of these species follows largely from their trigonal bipyramidal geometry. In conjunction with earlier calculations, the present study provides a broad overview of spin density profiles in iron-oxo species in general. Iron-oxo d(pi)-p(pi) interactions invariably result in a substantial spin density on the oxygen, which in turn may be significantly tuned by hydrogen bonding interactions. The oxygen spin densities are smaller in analogous manganese-oxo species, indicating that manganese is less adept at pi-bonding than iron, which parallels earlier findings on porphyrin systems. The Fe(III)-S/Se spin density profiles provide one of the first confirmations in a transition metal context of Schleyer's prediction that the heavier p-block elements are as effective as their second-row congeners in terms of their pi-donating ability.

Ferric Compounds↗
PubMed2005

The challenge of being straight: explaining the linearity of a low-spin [FeNO]7 unit in a tropocoronand complex.

We have carried out a density functional theory study of the S = 1/2 [FeNO]7 tropocoronand complex, Fe(5,5-TC)NO, as well as of some simplified models of this compound. The calculations accurately reproduce the experimentally observed trigonal-bipyramidal geometry of this complex, featuring a linear NO in an equatorial position and a very short Fe-N(NO) distance. Despite these unique structural features, the qualitative features of the bonding turn out to be rather similar for Fe(5,5-TC)NO and [FeNO]7 porphyrins. Thus, there is a close correspondence between the molecular orbitals (MOs) in the two cases. However, there is a critical, if somewhat subtle, difference in the nature of the singly occupied MOs (SOMOs) between the two. For square-pyramidal heme-NO complexes, the SOMO is primarily Fe d(z)2-based, which favors sigma-bonding interactions with an NO pi orbital, and hence a bent FeNO unit. However, for trigonal-bipyramidal Fe(5,5-TC)(NO), the SOMO is best described as primarily Fe d(x2-z2) in character, with the Fe-N(NO) vector being identified as the z direction. Apparently, such a d orbital is less adept at sigma bonding with NO and, as such, pi bonding dominates the Fe-NO interaction, leading to an essentially linear FeNO unit and a short Fe-N(NO) distance.

Ferric Compounds↗
PubMed2005

Modeling side-on NO coordination to type 2 copper in nitrite reductase: structures, energetics, and bonding.

DFT calculations reveal the existence of metastable side-on {CuNO}10 and {CuNO}11 species relevant to the type 2 copper site of nitrite reductase (CuNIR). Side-on NO coordination seems especially favorable in energy terms for the {CuNO}11 species. The {CuNO}11 geometry parameters also seem to be in better agreement with those reported for a crystallographically characterized CuNIR intermediate, relative to the {CuNO}10 parameters.

Catalysis↗
PubMed2005

Toward modeling H-NOX domains: a DFT study of heme-NO complexes as hydrogen bond acceptors.

Density functional theory calculations (PW91/STO-TZP, including basis-set superposition error corrections) have been used to evaluate hydrogen bond energies of five- and six-coordinate heme-NO complexes with phenol and imidazole, chosen as models for distal pocket tyrosine and histidine residues. The calculated interaction energies are approximately 2 kcal/mol for phenol and 3-4 kcal/mol for imidazole, which are 2-4 times smaller than the energies calculated for heme-O(2) complexes hydrogen-bonding with a distal histidine. Interestingly, the hydrogen bond energies are found to be very similar for five- and six-coordinate heme-NO complexes, which may be viewed as contrary to the interpretation of a recent observation on a bacterial H-NOX (Heme-Nitric oxide/OXygen-binding) protein with sequence homology to mammalian-soluble guanylate cyclase.

Algorithms↗
PubMed2005

Understanding the unexpected linearity of the trans-{Mn(NO)2}8 unit in a phthalocyanine complex: some thoughts on dinitrosylheme intermediates in biology.

Simple MO arguments provide a qualitative explanation for the near-linear ON-Mn-NO arrangement observed for the trans-{Mn(NO)2}8 anion [Mn(Pc)(NO)2]-, which is unexpected for an Enemark-Feltham electron count n>6. The metal center in this species may be described as low-spin d6("t2g6") and the two unpaired electrons occupy a pair of eu orbitals composed of NO(pi*) components, giving rise to a triplet ground state. In a certain sense, these eu SOMOs may be likened to the SOMO (singly occupied molecular orbital) of the allyl radical. The electronic structure of this species is quite different from that of diamagnetic dinitrosylheme intermediates, which have been spectroscopically characterized in synthetic studies as well as proposed for soluble guanylate cyclase and cytochrome c'. Some speculative remarks are offered as to why this proposal is not an unreasonable one from an electronic-structural perspective.

Electrons↗
PubMed2005

Electronic structure of cis-Mo(P)(NO)2, where P is a porphyrin: an organometallic perspective of metalloporphyrin-NO complexes.

This study presents a first MO analysis of the stereochemistry of cis-Mo(P)(NO)(2), where the Mo(NO)(2) unit eclipses a pair of opposite Mo-N bonds and also adopts a remarkable horseshoe-like conformation. In addition, we have uncovered a number of analogies--in terms of commonalities of metal-ligand orbital interactions--between the dinitrosylmetalloporphyrins, Fe(P)(NO)(2) and Mo(P)(NO)(2), and the two dialkylmetalloporphyrins, Ru(P)(CH(3))(2), and Zr(P)(CH(3))(2).

Ligands↗
PubMed2005

Metalloporphyrin-NO bonding: building bridges with organometallic chemistry.

DFT calculations in our laboratory and elsewhere have elucidated fundamental aspects of the structure and bonding of a variety of metalloporphyrin-diatomic complexes, including the biologically important heme CO, NO, and O(2) complexes. We have also studied some more exotic species such as metalloporphyrin-dinitrosyl, -dialkyl, and -diaryl complexes. In the course of this research, we discovered a number of unexpected similarities (isolobal analogies) between the bonding in metalloporphyrin-NO and organometallic compounds. Equally important, DFT calculations have played a significant role in advancing our understanding of selective diatomic ligand binding by heme proteins.

Hemeproteins↗
PubMed2004

A perspective of one-pot pyrrole-aldehyde condensations as versatile self-assembly processes.

Regarded as the classic one-pot synthetic route to symmetrical porphyrins for well over half a century, pyrrole-aldehyde cyclocondensations have yielded a cornucopia of nonporphyrin macrocycles, such as N-confused porphyrins, corroles, sapphyrins, and expanded porphyrins, and have thus emerged as versatile self-assembly processes. A highlight in this field is the remarkably general one-pot corrole synthesis. The manifold of intermediates generated in the anaerobic phase of a Lindsey-type synthesis have been viewed as a dynamic covalent self-assembly system. This raises the possibility that the addition of a suitable host may alter the equilibrium concentrations of these intermediates by molecular recognition and related phenomena and thus determine the major product formed after oxidative quenching.

Journal Article↗