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PubMed2006

Combining explicitly correlated R12 and Gaussian geminal electronic structure theories.

Explicitly correlated R12 methods using a single short-range correlation factor (also known as F12 methods) have dramatically smaller basis set errors compared to the standard wave function counterparts, even when used with small basis sets. Correlations on several length scales, however, may not be described efficiently with one correlation factor. Here the authors explore a more general MP2-R12 method in which each electron pair uses a set of (contracted) Gaussian-type geminals (GTGs) with fixed exponents, whose coefficients are optimized linearly. The following features distinguish the current method from related explicitly correlated approaches published in the literature: (1) only two-electron integrals are needed, (2) the only approximations are the resolution of the identity and the generalized Brillouin condition, (3) only linear parameters are optimized, and (4) an arbitrary number of (non-)contracted GTGs can appear. The present method using only three GTGs and a double-zeta quality basis computed valence correlation energies for a set of 20 small molecules only 2.2% removed from the basis set limit. The average basis set error reduces to 1.2% using a near-complete set of seven GTGs with the double-zeta basis set. The conventional MP2 energies computed with much larger quadruple, quintuple, and sextuple basis sets all had larger average errors: 4.6%, 2.4%, and 1.5%, respectively. The new method compares well to the published MP2-R12 method using a single Slater-type geminal (STG) correlation factor. For example, the average basis set error in the absolute MP2-R12 energy obtained with the exp(-r12) correlation factor is 1.7%. Correlation contribution to atomization energies evaluated with the present method and with the STG-based method only required a double-zeta basis set to exceed the precision of the conventional sextuple-zeta result. The new method is shown to always be numerically stable if linear dependencies are removed from the two-particle basis and the zeroth-order Hamiltonian matrix is made positive definite.

Journal Article↗
PubMed2003

Computational assessment of the electronic structure of 1-azacyclohexa-2,3,5-triene (3 delta 2-1H-pyridine) and its benzo derivative (3 delta 2-1H-quinoline) as well as generation and interception of 1-methyl-3 delta 2-1H-quinoline.

Treatment of a solution of 3-bromo-1-methyl-1,2-dihydroquinoline (9) and [18]crown-6 in furan or styrene with KOtBu followed by hydrolysis afforded a mixture of 1-methyl-1,2-dihydroquinoline (10) and 1-methyl-2-quinolone (11). If the reaction was performed in [D(8)]THF and the mixture was immediately analysed by NMR spectroscopy, 2-tert-butoxy-1-methyl-1,2-dihydroquinoline (17) was shown to be the precursor of 10 and 11. The structure of 17 is evidence for the title cycloallene 7, which arises from 9 by beta elimination of hydrogen bromide and is trapped by KOtBu to give 17 so fast that cycloadditions of 7 with furan or styrene cannot compete. Since this reactivity is unusual compared to the large majority of the known six-membered cyclic allenes, we performed quantum-chemical calculations on 8, which is the parent compound of 7, and the corresponding isopyridine 6 to assess the electronic nature of these species. The ground state of 6 was no longer an allene (6 a) but the zwitterion 6 b. In the case of 8, the allene structure 8 a is more stable than the zwitterionic form 8 b by only approximately 1 kcal mol(-1). These results suggest a high reactivity of 6 and 8 towards nucleophiles and explains the behaviour of 7. In addition to the ground states, the low-lying excited states of 6 and 8 were considered, which are represented by the diradicals 6 c and 8 c and, as singlets, lie above 6 b and 8 a by 19.1-24.8 and 14.4-17.7 kcal mol(-1), respectively.

Journal Article↗
PubMed2002

The first dirhodium tetracarboxylate molecule without axial ligation: new insight into the electronic structures of molecules with importance in catalysis and other reactions.

The first crystalline tetracarboxylato dirhodium paddlewheel complex with no axial ligation has been synthesized and structurally characterized. The compound, tetrakis(2,4,6-triisopropylbenzoato)dirhodium(II,II), Rh(2)(TiPB)(4), exhibits a Rh-Rh bond length of 2.3498(4) A. Interestingly, this is only ca. 0.02 A shorter than that in the corresponding bis-acetone adduct, 2.3700(4) A. The electronic spectrum exhibits two bands in the visible region; the low-energy band A has been previously attributed to a pi(Rh(2))-->sigma(Rh(2)) transition in various bis-adducts. The spectrum of Rh(2)(TiPB)(4)(acetone)(2) shows this band at 610 nm, while that of Rh(2)(TiPB)(4) is greatly displaced to 760 nm. This is very persuasive evidence that the assignment for this transition is correct.

Journal Article↗
PubMed2004

[Study on quantitative relationships between electronic structure and toxicities of phenyl-aldehydes and nitrogen-containing aromatic molecules].

The quantum chemical indexes of 13 phenyl-aldehydes and 18 nitrogen-containing aromatic molecules were calculated by PM3 method. Two quantitative structure-activity relationships of phenyl-aldehydes and nitrogen-containing aromatic molecules between quantum chemical indexes and toxicitives were obtained as follows: (1) for phenyl-aldehydes: pLD50 = -3.473 - 0.447 ELUMO, which indicated that the toxicities (pLD50) of phenyl-aldehydes would increase when energy of the lowest unoccupied molecular orbital (ELUMO) decrease, while the polarity of C = O group and dipolar moment increase; (2) for nitrogen-containing aromatic molecules: pIGC = 0.936 - 5.24 x 10(-5) E -0.300 DELH, which indicated that toxicities (pIGC) of nitrogen-containing aromatic molecules would increase when molecular energy E and the difference of HOMO and LUMO energy DELH decrease. The molecular energy E decreased mainly because of the enlargement of molecular volume which resulted in the enlargement of logP.

Benzaldehydes↗
PubMedDate not supplied

Electronic structure and cytotoxic activity of "half-mustard type" phenothiazines by MM3 and PM3 methods.

Among 54 cancer cell lines, colon-cancer cells were the most sensitive to six "half-mustard type" phenothiazines [7-12], followed by leukemia, melanoma, prostate-, CNS-, breast-, lung-, renal and ovarian cancer cells. The distribution of electrostatic potential (ESP) of "half-mustard type" phenothiazines [7-12] suggests that the ESP surface of urea site is important for the interaction between "half-mustard type" phenothiazines [7-12] and target cancer cell structures (or DNA base sequence). Actually, the urea site of "half-mustard type" phenothiazines displayed extensive variability in the energy of lone pair orbital and net atomic charges of N1, 0 and N3 atoms.

Algorithms↗
PubMed2005

Synergy of intramolecular hydrogen-bonding network in myo-inositol 2-monophosphate: theoretical investigations into the electronic structure, proton transfer, and pKa.

This work demonstrates the pivotal role that an intramolecular hydrogen-bonding network (intra-HBN) plays in the determination of the conformation of myo-inositol 2-monophosphate (Ins(2)P1), a member of the inositol phosphate family of compounds, which are important participants in the role that phosphates play in biological and environmental chemistry. For biologically significant compounds that contain phosphate and hydroxyl groups, Ins(2)P1 is a model system for studying both the primary forces that determine their conformations and their chemical properties from the effect of phosphate group addition. We performed ab initio calculations to determine the intra-HBN within important thermally accessible conformations for neutral Ins(2)P1 and its anions, Ins(2)P1(1-) and Ins(2)P1(2-). The results show that the global minima prefer 1a/5e structures where the phosphate group is in the axial position with all -OH groups in the equatorial positions. The calculations of transition state structures for ring inversion at each ionization state predict an activation energy of 18.16 kcal/mol for the neutral species in water, while the activation energy is lower for the charged compounds, 15.62 kcal/mol for Ins(2)P1(1-) and 12.48 kcal/mol for Ins(2)P1(2-). The pK(a) values of Ins(2)P1 were calculated by modeling the solvent as a polarizable continuum medium (PCM) and as explicit solvent molecules. These values are in good agreement with experimental data. A novel four-center pattern of hydrogen bonding was found to stabilize the system. The intramolecular proton transfer across a low barrier hydrogen bond between the charged phosphate and hydroxyl groups was found to occur under standard conditions with an activation energy that is less than 0.5 kcal/mol.

Electrons↗
PubMed2005

Geometric and electronic structures of multiple-decker one-end open sandwich clusters: Eu(n)(C8H8)n- (n = 1-4).

We have measured the photoelectron spectra of the multiple-decker 1:1 sandwich clusters of Eu(n)(COT)n- (n = 1-4; COT = 1,3,5,7-cyclooctatetraene), synthesized in the gas phase, and studied theoretically the bonding scheme, charge distribution, valence orbital energies, and photodetachment energies. We calculated the ground electronic state X- and the first excited electronic state A-, both of which have strong ionic bonding and a characteristic charge distribution. Moreover, we found that the valence orbital energies of Eu (6s) and COT (L delta) depend strongly on cluster size and their positions in the clusters. With the calculated vertical detachment energies for these valence orbitals, we assigned the peaks in the experimental photoelectron spectra and analyzed the origin of their interesting behavior by employing simple point charge models. From these analyses, it became clear that the characteristic behavior of the spectra is due to the strong ionic bonding and the charge distribution. In addition, using the point charge models, we estimated the vertical detachment energies of the one-dimensional polymer [Eu(COT)]infinity-.

Journal Article↗
PubMed2006

Ab initio study of the electronic structure of the crystalline high-mobility organic semiconductor 1,4-diiodobenzene.

We use ab initio crystalline calculations to explore the role of iodine in determining the properties of 1,4-diiodobenzene. The results strongly suggest that the large halogen is an important or perhaps the dominant determinant of the ability of diiodobenzene to transport holes. We conjecture that the high mobility of diiodobenzene is due to a combination of electronic and phononic effects, both influenced by the presence of the iodine.

Chemical Phenomena↗
PubMed1995

Determination of haem electronic structure in cytochrome b5 and metcyanomyoglobin.

The paramagnetic shifts of 13C nuclei positioned alpha to the haems in the A and B forms of rat cytochrome b5 and in metcyanomyoglobin have been analysed in terms of molecular orbitals based on D4h symmetry with a rhombic perturbation. The contribution to the 13C shifts from pseudocontact interactions is calculated from parameters obtained for a metal-centred dipolar shift tensor by fitting 1H shifts. The effect of electron delocalisation onto the vinyl groups of these haems b is separated with reference to the shifts of the vinyl beta carbons. In each case, it was found that the orientation of the magnetic axes in the plane of the haem is rotated away from the iron-nitrogen vectors in the opposite sense to the rotation of the rhombic perturbation and the molecular orbitals. The orientation of the orbitals is closely aligned with the normal to the single His ligand in metcyanomyoglobin, and with the average of the two normals in the bis-His cytochrome b5. It is concluded that the in-plane anisotropy of haems b is dominated by the orientation of the axial ligands in a similar manner to that in haems c and that the approximations used are weakened, but not invalidated, by the presence of partially conjugated vinyl groups.

Animals↗
PubMed2001

1H and 13C NMR investigation of the influence of nonligated residue contacts on the heme electronic structure in cyanometmyoglobin complexes reconstituted with centro- and pseudocentrosymmetric hemins.

The 1H and 13C chemical shifts for the heme methyls of low-spin, ferric sperm whale cyanometmyoglobin reconstituted with a variety of centrosymmetric and pseudocentrosymmetric hemins have been recorded and analyzed to shed light on the nature of heme-protein contacts, other than that of the axial His, that modulate the rhombic perturbation to the heme's in-plane electronic asymmetry. The very similar 1H dipolar shifts for heme pocket residues in all complexes yield essentially the same magnetic axes as in wild type, and the resultant dipolar shifts allow the direct determination of the heme methyl proton and 13C contact shifts in all complexes. It is demonstrated that, even when the magnetic axes and anisotropies are known, the intrinsic uncertainties in the orientational parameters lead to a sufficiently large uncertainty in dipolar shift that the methyl proton contact shifts are inherently significantly less reliable indicators of the unpaired electron spin distribution than the methyl 13C contact shifts. The pattern of the noninversion symmetry in 13C contact shifts in the centro- or pseudocentrosymmetric hemes is shown to correlate with the positions of aromatic rings of Phe43(CD1) and His97(FG3) parallel to, and in contact with, the heme. These results indicate that such pi-pi interactions significantly perturb the in-plane asymmetry of the heme pi spin distribution and cannot be ignored in a quantitative interpretation of the heme methyl 13C contact shifts in terms of the axial His orientation in b-type hemoproteins.

Animals↗
PubMed1974

The pairwise correlated generalized valence bond model of electronic structure I; the estimation of pair energies from orbital overlaps.

A new method for the accurate a priori calculation of atomic and molecular energies is proposed. The new method agrees with experiment to within less than 1 kcal/mole in all cases examined thus far, and is applicable to excited states and to transition states for chemical reactions. Since the new method corrects the results of generalized valence bond calculations for the effects of electron pair correlations, we call the new method the pairwise correlated generalized valence bond method.

Journal Article↗
PubMed2006

Two-photon photoemission spectroscopy study of 1,3-butadiene on Cu(111): electronic structures and excitation mechanism.

The characteristics of 1,3-butadiene (C(4)H(6)) adsorbed on Cu(111) were investigated with temperature-programmed desorption (TPD) and two-photon photoemission spectroscopy (2PPE). Dosed at 90 K, the work function drops by 0.4 eV and TPD provides no evidence for dissociation, but there are four coverage-dependent local maxima located at 195, 135, 121, and 115 K. From the 2PPE spectra, three unoccupied electronic states of the C(4)H(6)-Cu(111) system were identified: the LUMO (pi(1)*, 2a(u)), LUMO + 1 (pi(2)*, 2b(g)), and LUMO + 2 (sigma*, 7b(u)), lying 1.3, 3.4, and 4.8 eV above the Fermi level, respectively. Although the excitation mechanisms for the LUMO and LUMO + 1 are substrate mediated, the excitation of the LUMO + 2 is attributed to intramolecular excitation.

Journal Article↗
PubMed2005

Molecular and electronic structure of five-coordinate complexes of iron(II/III) containing o-diiminobenzosemiquinonate(1-) pi radical ligands.

The reaction of the ligand N-phenyl-1,2-benzenediamine (N-phenyl-o-phenylenediamine), H2[L(PDI)], in dry acetonitrile with [FeIII(dmf)6](ClO4)3 (dmf = N,N-dimethylformamide) affords the dimer (mu-NH,NH)[FeIII(L(ISQ))(L(PDI))]2 (1), where (L(ISQ))*- represents the pi radical monoanion N-phenyl-o-diiminobenzosemiquinonate and (L(PDI))2- is its one-electron-reduced, closed-shell form. Complex 1 possesses a diamagnetic ground-state St = 0. Addition reactions of tri-n-butylphosphane, tert-butyl isocyanide, cyclohexyl isocyanide, 4,5-diphenylimidazole, and 4-(1-phenylpentyl)pyridine with 1 in acetonitrile or toluene yields [FeII(L(ISQ))2(PBu3)] (2), [Fe(II)(L(ISQ))2(CN-tBu)] (4), [FeII(L(ISQ))2(CNCy)] (5), [FeIII(L(ISQ))2(Ph2Im)] (6), and [FeIII(L(ISQ))(L(PDI))(BuPhCH-py)].BuPhCH-py (7). Oxidation of 1 with iodine affords [FeIII(L(ISQ))2I] (3), and oxidation of 2 with ferrocenium hexafluorophosphate yields [FeIII(L(ISQ))2(PBu3)](PF6) (2ox). The structures of complexes 2, 2ox, 3, 5, 6, and 7 have been determined by X-ray crystallography at 100(2) K. Magnetic susceptibility measurements and EPR, UV-vis, and Mössbauer spectroscopy have established that mononuclear complexes containing the [FeII(L(ISQ))2X] chromophore (2, 4, 5) are diamagnetic (St = 0) whereas those with an [FeIII(L(ISQ))2X]n chromophore (3, 2(ox), 6) are paramagnetic (St = 1/2) and those with an [FeIII(L(ISQ))(L(PDI))X] chromophore (7) possess an St = 1 ground state. It is established that all ferric species have an intrinsic intermediate spin (SFe = 3/2) which is intramolecularly antiferromagnetically coupled to one or two (L(ISQ))*- ligand radicals yielding an St = 1 (7) or St = 1/2 (2ox, 3, 6) ground state, respectively. In the ferrous complexes 2, 4, and 5 the intrinsic spin at the iron ion is either low spin (SFe = 0) or intermediate spin (SFe = 1). Antiferromagnetic coupling between two radicals (L(ISQ))*- or, alternatively, between the intermediate spin ferrous ion and two radicals yields then the observed diamagnetic ground state. In 1 two [FeIII(L(ISQ))(L(PDI))] halves with S = 1 couple antiferromagnetically affording an St = 0 ground state.

Journal Article↗
PubMed2002

meso Substituent effects on the geometric and electronic structures of high-spin and low-spin iron(III) complexes of mono-meso-substituted octaethylporphyrins.

Introduction of a single meso substituent into ClFe(III)(OEP) or K[(NC)(2)Fe(OEP)] results in significant changes in the geometric and/or spectroscopic properties of these complexes. The mono-meso-substituted iron(III) complexes ClFe(III)(meso-Ph-OEP), ClFe(III)(meso-n-Bu-OEP), ClFe(III)(meso-MeO-OEP), ClFe(III)(meso-Cl-OEP), ClFe(III)(meso-NC-OEP), ClFe(III)(meso-HC(O)-OEP), and ClFe(III)(meso-O(2)N-OEP) have been isolated and characterized by their UV/vis and paramagnetically shifted (1)H NMR spectra. The structures of both ClFe(III)(meso-Ph-OEP) and ClFe(III)(meso-NC-OEP) have been determined by X-ray crystallography. Both molecules have five-coordinate structures typical for high-spin (S = 5/2) iron(III) complexes. However, the porphyrins themselves no longer have the domed shape seen in ClFe(III)(OEP), and the N(4) coordination environment possesses a slight rectangular distortion. These high-spin, mono-meso-substituted iron(III) complexes display (1)H NMR spectra in chloroform-d solution which indicate that the conformational changes seen in the solid-state structures are altered by normal molecular motion to produce spectra consistent with C(s) molecular symmetry. In pyridine solution the high-spin six-coordinate complexes [(py)ClFe(III)(meso-R-OEP)] form. In methanol solution in the presence of excess potassium cyanide, the low-spin six-coordinate complexes K[(NC)(2)Fe(III)(meso-R-OEP)] form. The (1)H NMR spectra of these show that electron-donating substituents produce an upfield relocation of the meso-proton chemical shifts. This relocation is interpreted in terms of increased contribution from the less common (d(xz),d(yz))(4)(d(xy))(1) ground electronic state as the meso substituent becomes more electron donating.

Crystallography, X-Ray↗
PubMed1997

Electronic Structure of the Lowest Excited States of Cr(CO)(4)(2,2'-bipyridine): A CASSCF/CASPT2 Analysis.

The visible and UV absorption spectra of Cr(CO)(4)(bpy) are interpreted according to CASPT2 calculations based on CASSCF reference wave functions using atomic natural orbital (ANO) basis sets. The excitation energies of the lowest singlet MLCT (metal-to-ligand-charge-transfer) states range between 12 630 and 17 580 cm(-)(1). They originate in the excitation of chromium d electrons to the lowest pi(bpy) orbital of b(2) local symmetry. Dipole transition moments calculated for individual MLCT transitions show that the only transition expected to contribute significantly to the intense absorption band in the visible spectral region is the a(1)A(1) --> b(1)A(1) transition calculated at 17 580 cm(-)(1). This result agrees very well with the experimental spectra recorded in weakly solvating C(2)Cl(4), characterized by a band at 17 700 cm(-)(1). The low-energy emission band at 12 850 cm(-)(1) has been attributed to the lowest a(3)B(2) state calculated at 12 560 cm(-)(1). The next set of excited states corresponding to 3d --> pi(bpy,a)()2 excitations range between 25 370 and 26 200 cm(-)(1) for the singlets and between 24 630 and 25 750 cm(-)(1) for the triplets. The singlet excited states corresponding to d --> d excitations are calculated between 29 650 and 37 360 cm(-)(1). These results show that the intense absorption in the near-UV spectral region originates in strongly overlapping absorption bands due to closely spaced transitions into MLCT (a(2)) and dd excited states, respectively. The c(1)B(2) excited state corresponding to the 3d(xz)() --> 3d(z)()()2 excitation, proposed as photoactive in the mechanism of the efficient CO loss under irradiation at 27 630 cm(-)(1), is calculated at 36 320 cm(-)(1) and is far too high to be directly populated in these photochemical studies. Its mixing with one or several low-lying (singlet) MLCT states at the early stage of the reaction path could be responsible for the observed primary reaction. A comparison between the excitation energies of the lowest singlet states of Cr(CO)(4)(bpy) and Cr(CO)(4)(dab) is reported. The most significant feature is the lowering of the MLCT excited states on going from the bpy-containing molecule to its dab (1,4-diaza-1,3-butadiene) analog.

Journal Article↗
PubMed2003

Electronic structure of iron chlorins: characterization of bis(l-valine methyl ester)(meso-tetraphenylchlorin)iron(III)triflate and bis(l-valine methyl ester)(meso-tetraphenylchlorin)iron(II).

The synthesis and characterization of the two iron chlorin complexes [Fe(III)(TPC)(NH(2)CH(CO(2)CH(3))(CH(CH(3))(2)))(2)]CF(3)SO(3) (1) and Fe(II)(TPC)[(NH(2)CH(CO(2)CH(3))(CH(CH(3))(2))](2) (2) are reported. The crystal structure of complex 1 has been determined. The X-ray structure shows that the porphyrinate rings are weakly distorted. The metal-nitrogen distances to the reduced pyrrole N(4), 2.034(4) A, and to the pyrrole trans to it N(2), 2.012(4) A, are longer than the distances to the two remaining nitrogens [N(1), 1.996(4) A, and N(3), 1.984(4) A], leading to a core-hole expansion of the macrocycle due to the reduced pyrrole. The (1)H NMR isotropic shifts at 20 degrees C of the different pyrrole protons of 1 varied from -0.8 to -48.3 ppm according to bis-ligated complexes of low-spin ferric chlorins. The EPR spectrum of [Fe(TPC)(NH(2)CH(CO(2)CH(3))(CH(CH(3))(2)))(2)]CF(3)SO(3) (1) in solution is rhombic and gives the principal g values g(1) = 2.70, g(2) = 2.33, and g(3) = 1.61 (Sigmag(2) = 15.3). These spectroscopic observations are indicative of a metal-based electron in the d(pi) orbital for the [Fe(TPC)(NH(2)CH(CO(2)CH(3))(CH(CH(3))(2)))(2)]CF(3)SO(3) (1) complex with a (d(xy))(2)(d(xz)d(yz))(3) ground state at any temperature. The X-ray structure of the ferrous complex 2 also shows that the porphyrinate rings are weakly distorted. The metal-nitrogen distances to the reduced pyrrole N(4), 1.991(5) A, and to the pyrrole trans to it N(2), 2.005(6) A, are slightly different from the distances to the two remaining nitrogens [N(1), 1.988(5) A, and N(3), 2.015(5) A], leading to a core-hole expansion of the macrocycle due to the reduced pyrrole.

Crystallography, X-Ray↗
PubMed2004

Crystal, molecular and electronic structure of N,N'-diphenyl-N,N'-bis(2,4-dimethylphenyl)-(1,1'-biphenyl)-4,4'-diamine and the corresponding radical cation.

Oxidation of N,N'-diphenyl-N,N'-bis(3-methylphenyl)-(1,1'-biphenyl)-4,4'-diamine (TPD, 1 a) and N,N'-diphenyl-N,N'-bis(2,4-dimethylphenyl)-(1,1'-biphenyl)-4,4'-diamine (1 b) with SbCl(5) affords the corresponding radical cations quantitatively. The crystal and molecular structure of 1 b and [1 b]SbCl(6), the first tetraphenyl benzidene derivatives to be characterised crystallographically in both the neutral and radical cation states, reveal molecular parameters in agreement with the predictions made on the basis of DFT studies. Analysis of the NIR transition in the radical cations [1](+) (.) allows an estimate of the electronic coupling parameter V (1 a(+) (.) 3200 cm(-1); 1 b(+) (.) 3300 cm(-1)), the reorganisation energy lambda(1 a(+) (.) 7500 cm(-1); 1 b(+) (.) 7800 cm(-1)), and the linear coupling constant l (1 a(+) (.) 3100 cm(-1); 1 b(+) (.) 2700 cm(-1)) of the symmetric mode.

Journal Article↗