Density Functional Theory Electronic Structure Research Articles

Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase.

The binding of NO to the iron heme in guanylate cyclase and other heme proteins induces the cleavage of the proximal histidine bonded to the metal. In this study we assess by means of density functional theory (DFT) electronic structure calculations the role of H-bonding to histidine in the modulation of this effect. We have considered in the first place a model of the isolated active site coordinated with imidazole and imidazolate to mimic the effects of a very strong H-bond. We have also investigated four selected ferrous heme proteins with different proximal histidine environments: the O(2) sensing FixL, horseradish peroxidase C, and the alpha and beta subunits of human hemoglobin. Our results indicate that polarization and charge transfer effects associated with H-bonding to the proximal histidine play a fundamental role in the modulation of the NO trans effect in heme proteins. We also find computational evidence suggesting that protein structural constraints may affect significantly the cleavage of the Fe-His bond.

Jahn–Teller triplet excited state structures and spectra of zinc complexes of porphyrin and phthalocyanine: A density functional theory study

Density functional theory (DFT) electronic structure calculations were carried out to predict the triplet Jahn–Teller distorted structures and energetics for zinc complexes of porphyrin (ZnP), tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine. The D4h square planar structures in the ground state are found to distort along the b1g mode leading to the D2h rectangle structures in the lowest triplet state. Time-dependent DFT calculations were also carried out to interpret the observed triplet–triplet spectra and to quantify the effects of meso-tetraaza substitutions and tetrabenzo annulations on ZnP. The computed triplet–triplet excitation energies and oscillator strengths are in good agreement with experiment. The effects of meso-tetraaza substitutions and tetrabenzo annulations on the triplet excited state structures and spectra are discussed in detail.

Spectroscopic and computational studies on [(PhTt(tBu))2Ni2(mu-O)2]: nature of the bis-mu-oxo (Ni3+)2 diamond core.

Spectroscopic and density functional theory (DFT) electronic structure computational studies on a binuclear bis-mu-oxo bridged (Ni(3+))(2) complex, [(PhTt(t(Bu))(2)Ni(2)(mu-O)(2)] (1), where (PhTt(t(Bu)) represents phenyl-tris((tert-butylthio)methyl)borate, are presented and discussed. These studies afford a detailed description of the Ni(2)O(2) core electronic structure in bis-mu-oxo (Ni(3+))(2) dimers and provide insight into the possible role of the (PhTt(t(Bu)) thioether ligand in the formation of 1 from a Ni(1+) precursor by O(2) activation. From a normal coordinate analysis of resonance Raman data, a value of k(Ni)(-)(O) = 2.64 mdyn/A is obtained for the Ni-O stretch force constant for 1. This value is smaller than k(Cu)(-)(O) = 2.82-2.90 mdyn/A obtained for bis-mu-oxo (Cu(3+))(2) dimers possessing nitrogen donor ligands, indicating a reduced metal-oxo bond strength in 1. Electronic absorption and magnetic circular dichroism spectroscopic techniques permit identification of several O-->Ni and S-->Ni charge transfer (CT) transitions that are assigned on the basis of DFT calculations. The dominant O-->Ni CT transition of 1 occurs at 17 700 cm(-)(1), red-shifted by approximately 7000 cm(-)(1) relative to the corresponding transition in bis-mu-oxo (Ni(3+))(2) dimers with nitrogen donor ligands. This red-shift along with the relatively low value of k(Ni)(-)(O) are due primarily to the presence of the thioether ligands in 1 that greatly affect the compositions of the Ni(2)O(2) core MOs. This unique property of the thioether ligand likely contributes to the reactivity of the Ni center in the precursor [(PhTt(t(Bu))Ni(1+)CO] toward O(2). DFT computations reveal that conversion of a hypothetical side-on peroxo (Ni(2+))(2) dimer, [(PhTt(t(Bu))(2)Ni(2)(mu-eta(2):eta(2)-O(2))], to the bis-mu-oxo (Ni(3+))(2) dimer 1 is energetically favorable by 32 kcal/mol and occurs without a significant activation energy barrier (DeltaH++) = 2 kcal/mol).

Anisotropic valence→core x-ray fluorescence from a [Rh(en)3][Mn(N)(CN)5]⋅H2O single crystal: Experimental results and density functional calculations

High resolution x-ray fluorescence spectra have been recorded for emission in different directions from a single crystal of the compound [Rh(en)3][Mn(N)(CN)5]⋅H2O. The spectra are interpreted by comparison with density functional theory (DFT) electronic structure calculations. The Kβ″ line, which is strongly polarized along the Mn–N axis, can be viewed as an N(2s)→Mn(1s) transition, and the angular dependence is understood within the dipole approximation. The so-called Kβ2,5 region has numerous contributions but is dominated by Mn(4p) and C(2s)→Mn(1s) transitions. Transition energy splittings are found in agreement with those of calculated occupied molecular orbitals to within 1 eV. Computed relative transition probabilities reproduce experimentally observed trends.

Density functional theory predictions of anharmonicity and spectroscopic constants for diatomic molecules

The reliability of density functional theory and other electronic structure methods is examined for anharmonicities and spectroscopic constants of the ground electronic states of several diatomic molecules. The equilibrium bond length re, harmonic vibrational frequency ωe, vibrational anharmonicity ωexe, rotational constant Be, centrifugal distortion constant D̄e, and vibration-rotation interaction constant αe have been obtained theoretically for BF, CO, N2, CH+, and H2. Predictions using Hartree–Fock, coupled-cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples [CCSD(T)], and various density functional methods (S-VWN, BLYP, and B3LYP) have been made using the 6-31G*, aug-cc-pVDZ, and aug-cc-pVTZ basis sets and compared to experimental values. Density functional theory predictions of the spectroscopic constants are reliable (particularly for B3LYP) and often perform as well as the more expensive CCSD and CCSD(T) estimates.

Ground state electronic structures and spectra of zinc complexes of porphyrin, tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study

Density functional theory (DFT) electronic structure calculations were carried out to predict the structures and ground-state spectra for zinc complexes of porphyrin (ZnP), tetraazaporphyrin (ZnTAP), tetrabenzoporphyrin (ZnTBP), and phthalocyanine (ZnPc). All four porphyrins are found to have stable D4h structures. Structurally, meso-tetraaza substitutions significantly reduce the central hole in ZnTAP and ZnPc compared to ZnP. The excitation energies and oscillator strengths, computed by time-dependent DFT, provide a good account of the observed spectra of all four compounds. The TDDFT spectrum of ZnPc has a number of bands in the Soret region, in agreement with the experimental spectra that have been determined through spectral deconvolution. The low energy n→π* transition (Q′) reported for ZnPc, however, was not found in the computed spectrum. The effects of meso-tetraaza substitutions and tetrabenzo annulations on the spectrum of ZnP are discussed.

Triplet Excited States of Free-Base Porphin and Its β-Octahalogenated Derivatives

Density functional theory (DFT) electronic structure calculations were carried out to predict the structures, energetics, and triplet−triplet (T−T) spectra for the low-lying triplet states of free-base porphin (PH2) and its β-octahalogenated derivatives (β-PH2X8; X = F, Cl, Br). The lowest triplet excited state of PH2 and β-PH2X8 was found to retain D2h symmetry with stretched Cβ−Cβ and Cβ−Cm bond distances. For free-base porphin, the singlet−triplet (S0−T1) gap obtained with the B3LYP functional was in excellent agreement with the experimental phosphorescence value. Excitation energies computed by time-dependent DFT also provided a fine account of the observed T−T spectrum. β-Halogenation had little effect on the singlet−triplet gaps of porphin. The S0−T1 and S0−T2 splittings for β-PH2X8 were within 0.1 eV of the corresponding splittings in the unsubstituted porphin. All bands in the T−T spectra of β-PH2X8 were predicted to be significantly (up to 0.65 eV) red-shifted in comparison to corresponding bands...

Developments in the density-functional theory of electronic structure

Density-functional theory has provided a robust and practical framework for microscopic calculations of electronic structure and atomic bonding in condensed matter. On the microscopic level, it is being extended to situations such as nonconventional bonds, dielectrics, time-dependent phenomena, excitations, and novel magnetic systems. It is also being incorporated into multiscale modelling by coupling it to coarse-grained and continuum simulations of materials.

Theoretical studies of pentene cracking on zeolites: C–C β-scission processes

The C–C bond-breaking step of pentene adsorbed on a model zeolite cluster is examined using ab initio and density functional theory (DFT/B3LYP) electronic structure techniques as an example of the β-scission process that arises in cracking of alkanes and alkenes. After pentene has been protonated by the acid site, the reactant for the cracking process corresponds to a pentyl cation covalently bound to the oxygen of the zeolite, ZO −–C 5H + 11. The product of the C–C bond-breaking process is propene plus an ethyl cation bound to a neighboring oxygen. The energy of the transition state relative from B3LYP calculations is 60 kcal/mol relative to the pentyl cationic reactant. For the case of the branched olefin methyl pentene, the transition state energy is slightly lower (55 kcal/mol), but the overall reaction energy is essentially the same as for pentene. The results are compared to the case of the gas phase pentyl carbenium ion.

DFT and ab Initio Study of the Unimolecular Decomposition of the Lowest Singlet and Triplet States of Nitromethane

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C−NO2 bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. We perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C−N bond distance with 12−16 kcal/mol lower energy than does MCSCF. In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by DFT methods based on Becke's 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF ...

TheRate: Program forab initio direct dynamics calculations of thermal and vibrational-state-selected rate constants

We introduce TheRate THEoretical RATEs , a complete . application program with a graphical user interface GUI for calculating rate constants from first principles. It is based on canonical variational transition-state . theory CVT augmented by multidimensional semiclassical zero and small . curvature tunneling approximations. Conventional transition-state theory TST with one-dimensional Wigner or Eckart tunneling corrections is also available. Potential energy information needed for the rate calculations are obtained from ab initio molecular orbital andror density functional electronic structure theory. Vibrational-state-selected rate constants may be calculated using a diabetic model. TheRate also introduces several technical advancements, namely the focusing technique and energy interpolation procedure. The focusing technique minimizes the number of Hessian calculations required by distributing more Hessian grid points in regions that are critical to the CVT and tunneling calculations and fewer Hessian grid points elsewhere. The energy interpolation procedure allows the use of a computationally less demanding electronic structure theory such as DFT to calculate the Hessians and geometries, while the energetics can be improved by performing a small number of single-point energy calculations along the MEP at a more accurate level of theory. The CH q H l CH q H reaction is used as a model to demonstrate usage of the 43 2 program, and the convergence of the rate constants with respect to the number of electronic structure calculations. Q 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1039)1052, 1998

Reactivity of niobium clusters with nitrogen and deuterium

Absolute rate coefficients are reported for reactions of Nbn clusters (n=2–20) with D2 and N2 at 280, 300, and 370 K. Most clusters are highly reactive but there are conspicuous exceptions at n=8, 10, and 16 for both D2 and N2. The origin of this trend in reactivity with cluster size and the reason why D2 and N2 show similar trends are discussed. Density functional theory (DFT) electronic structure calculations have been used to investigate the details of the reactions for the smallest clusters Nb2 and Nb8 with H2 and N2. The steric and electronic requirements for dissociation of H2 and N2 are described in terms of frontier orbital interactions. The main conclusion from the DFT calculations is that complete dissociation of H2 or N2 requires charge transfer by transit of an avoided crossing between neutral and ionic potentials. This idea is extended to larger clusters by using a simple charge transfer model that predicts an inverse correlation between reactivity and an appropriately defined effective ionization potential. Such a correlation is observed and indicates that the effective ionization potential is the dominant influence on reactivity.

Elongated Dihydrogen Complexes: A Combined Electronic DFT + Nuclear Dynamics Study of the [Ru(H···H)(C5H5)(H2PCH2PH2)]+ Complex

A study on a modeled version of the complex [Ru(H···H)(C5Me5)(dppm)]+ has been performed both at electronic structure level and including quantum treatment of nuclei. Density functional theory (DFT) electronic structure calculations alone fail to reproduce the experimentally reported geometry of the elongated dihydrogen ligand of the complex, even though the rest of the complex is satisfactorily described. Quantum nuclear motion calculations manage to correctly explain the geometries found experimentally by means of neutron diffraction measurements. Isotopic effects are predicted for the hydrogen−hydrogen distance of the elongated dihydrogen ligand depending on its isotopic composition. Moreover, the temperature dependence of the J(H,D) coupling constant is also interpreted successfully on the grounds of varying population of the vibrational excited states of the Ru−H2 unit.

Density-Functional Theory of the Electronic Structure of Molecules

Recent fundamental advances in the density-functional theory of electronic structure are summarized. Emphasis is given to four aspects of the subject: (a) tests of functionals, (b) new methods for determining accurate exchange-correlation functionals, (c) linear scaling methods, and (d) developments in the description of chemical reactivity.