MO Calculations Research Articles

Unusual Saddle‐like Structure of (2‐MeOC6H4CS)2S: Theoretical Studies and Comparison with its Oxygen Isologues

AbstractCompound (2‐MeOC6H4CS)2S (1) showed an unusual saddle structure in which the –C(=S)–S–C(=S)– moiety is planar and two benzene rings lie a face‐to‐face and the distances (3.07 Å) between the central sulfur atom and two 2‐methoxy oxygen atoms are within the sum of van der Waals radii of the both atoms. However, the results of MO calculation at the B3LYP/6‐311+G(2d, p) level showed no orbital interaction between both atoms. From the results of the calculations at the MP2 level, it was deduced that the crystal packing effect is important for such densely packed crystal, due to its less effective volume. On the other hand, the para‐methoxy derivative (4‐MeOC6H4CS)2S (2) in which the two methoxy oxygen atoms are not able to contact with the central sulfur atom shows an L‐shaped structure in which the –C(=S)–S–C(=S)– moiety is not planar. The –C(=O)–S–C(=S)– moiety in compound (2‐MeOC6H4CO)(2‐MeOC6H4CS)S (3b) shows an L‐shaped structure, though the two methoxy oxygen atoms are in intramolecular contact with the central sulfur atom. The deep blue to green colors of compounds 1 and 2 and the deep violet color of compound 3b are due to transitions of the lone‐pair electrons in the HOMO (ψ87) of the thiocarbonyl sulfur atom to the LUMO (ψ89)and of those in the HOMO (ψ83) of the thiocarbonyl sulfur atom to the LUMO (ψ85), respectively.

Structure of 1-naphthol–water clusters in the S1 state studied by UV–IR fluorescence dip spectroscopy and ab initio molecular orbital calculations

IR spectra of trans-1-naphthol–(H2O)n (n=0–3) clusters in the S1 state were measured by UV–IR fluorescence dip spectroscopy. The observed dip spectra were compared with theoretical ones of various stable conformations predicted by ab initio MO calculations. From the comparison, linear (n=1) and cyclic hydrogen-bond structures (n=2 and 3) were concluded. The relation between the structures and photochemical reactivity was discussed.

A Study on the Relationship between the Twisted π-Conjugate System of 1,5-Diaryl-1,5-diazapenta-1,3-dienes and Their Photophysical Properties

Abstract One-pot treatment of commercially available 1,3,3-tributoxy-2-cyanopropene with 2 equivalents of primary aromatic amines readily afforded 1,5-diaryl-1,5-diaza-3-cyanopenta-1,3-dienes. UV properties varied as steric size of the ortho-substituent in the N-aryl units increased. X-ray crystallographic analyses indicated preferable conformation of these compounds, and the twist angles between 1,5-diazapentadiene and aromatic units were measured. The relationship between the twisted angles and UV absorptions was rationalized by MO calculation, and the UV peak wavelengths are useful for the estimation of the twisted angles. A novel tetracoordinate diaryl-1,5-diazapentadiene was prepared. UV spectrum for its lithium complex in CHCl3 supported that the complex had a twisted conformation of the aryl units because the two etharial oxygen atoms coordinated to lithium cation.

ChemInform Abstract: The CH/π Hydrogen Bond: Implication in Chemistry

AbstractReview: 85 refs.

Synthesis of Carbazole‐Type D‐π‐A Fluorescent Dyes Possessing Solid‐State Red Fluorescence Properties

AbstractCarbazole‐type donor‐π‐acceptor (D‐π‐A) fluorescent dyes (SO1 and SO2), each containing a diphenylamino system as an electron‐donating group and a nitro moiety as an electron‐accepting group, have been designed and synthesized, and their photophysical properties in solution and in the solid state have been investigated. The absorption and fluorescence properties of SO1 and SO2 in solution are similar, and both dyes exhibited moderate fluorescence quantum yields. In the solid state, however, the dye SO2, with a butyl substituent on the carbazole ring, exhibited red fluorescence at around 620 nm, whereas the dye SO1, with no substituent on the carbazole ring, did not exhibit these solid‐state fluorescence properties. Furthermore, the dye SO2 exhibited weak mechanofluorochromic (MFC) properties: grinding of as‐recrystallized dyes induces slight bathochromic shifts of the fluorescence excitation and emission maxima. To elucidate the effects of molecular and crystal structures on the solid‐state fluorescence properties, we performed semiempirical molecular orbital calculations (PM3 and INDO/S) and single‐crystal X‐ray structural analysis. The X‐ray crystal structures of SO1 and SO2 demonstrated that a continuous intermolecular π‐stacking between the fluorophores was observable in the crystal structure of SO1, but not in that of SO2. The MO calculations revealed that SO1 and SO2 have similarly large dipole moments in the ground state (μg ≈ 8 D). The relationship between the observed solid‐state photophysical properties and the molecular and crystal structures of the carbazole‐type D‐π‐A fluorescent dyes are discussed on the basis of experimental results and MO calculations. It is found that the formation of a continuous intermolecular π‐stacking between the fluorophores causes a drastic fluorescence quenching in the solid state and that D‐π‐A fluorescent dyes with very large dipole moments can reduce the MFC properties, due to strong dipole–dipole interactions between the fluorophores in the solid state.

Transmission of Electronic Substituent Effects through a Benzene Framework: A Computational Study of 4-Substituted Biphenyls Based on Structural Variation

The transmission of substituent effects through a benzene framework has been studied by a novel approach, based on the structural variation of the Ph group in p-Ph-C(6)H(4)-X molecules. The molecular structures of many 4-substituted biphenyls were determined from MO calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. The twist angle between the phenyl probe (ring B) and the benzene framework carrying the substituent (ring A) was set at 90° to prevent π-electron transfer from one ring to the other and at 0° to maximize it. The structural variation of the probe is best represented by a linear combination of the internal ring angles, termed S(F)(BIPH(o)) and S(F)(BIPH(c)) for the orthogonal and coplanar conformations of the molecules, respectively. Regression analysis of these parameters using appropriate explanatory variables reveals a composite field effect, a substantial proportion of which is originated by resonance-induced π-charges on the carbon atoms of ring A. Field-induced polarization of the π-system of ring A also contributes to the structural variation of the probe. Thus, the S(F)(BIPH(o)) parameter is very well reproduced by a linear combination of the π-charges on the ortho, meta, and para carbons of ring A, an uncommon example of a quantitative relationship between molecular geometry and electron density distribution. Comparison of S(F)(BIPH(o)) with the gas-phase acidities of para-substituted benzoic acids shows that, while the deprotonating carboxylic probe is more sensitive to π-electron withdrawal than donation, the phenyl probe is equally sensitive to both. While the ability of the orthogonal biphenyl system to exchange π-electrons with the para substituent is the same as that of the benzene ring in Ph-X molecules, an increase by about 18% occurs when the conformation is changed from orthogonal to coplanar. The structural variation of the probe becomes more complicated, however. This is due to π-electron transfer from one ring to the other, which is shown to introduce quadratic terms in the regressions.

Functionalization of Diameter‐Sorted Semiconductive SWCNTs with Photosensitizing Porphyrins: Syntheses and Photoinduced Electron Transfer

Covalent functionalization of diameter sorted SWCNTs with porphyrins (MP), and photochemistry to establish nanotube diameter-dependent charge separation efficiencies are reported. The MP-SWCNT(n,m) [M=2H or Zn, and (n,m)=(7,6) or (6,5)] nanohybrids are characterized by a variety of spectroscopic, thermogravimetric, TEM imaging techniques, and also by DFT MO calculations. The thermogravimetric, Raman and fluorescence studies reveal the presence of a moderate number of porphyrins on the SWCNT surface. The MO results suggest charge separation (CS) via the excited state of MP. Time-resolved fluorescence studies reveal quenching of the singlet excited state of the MP with SWCNT(n,m), giving the rate constants of charge separation (k(CS)) in the range of (4-5)×10(9) s(-1). Nanosecond transient absorption measurements confirm the charge-separated radical cation and the radical anion as [MP(.+)-SWCNT(.-)] with their characteristic absorption bands in the visible and near-IR regions. The charge separated states persist for about 70-100 ns thus giving an opportunity to utilize them to build photoelectrochemical cells, which allowed us to derive the structure-reactivity relationship between the nature of porphyrin and diameter of the employed nanotubes.

Synthesis, Crystal Structure and DFT Study of 5-tert-Butyl-2-hydroxy-1,3-phenylene-bis(phenylmethanone)

The title compound C24H22O3, [common name: 4-tert-butyl-2,6-dibenzoylphenol (bdbpH)] (I), crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters a = 7.7633(3), b = 11.4457(6) and c = 21.5319(8) A, α = β = γ = 90o, Z = 4. In the crystal structure of I, the dihedral angles between the mean planes of the central phenyl ring and the two benzene rings are 71.3(1)° and 44.9(7)°. The two benzene rings are not coplanar with dihedral angles of 42.6(7)° between them. An intramolecular O–H···O hydrogen bond is observed in the asymmetric unit. The crystal packing is stabilized by weak intermolecular C–H···O interactions. Comparison of the optimized geometries by means of a density functional theory molecular orbital theoretical calculation at the B3LYP/6-31g(d) level with the corresponding crystal structures gives support to these observations. The electronic spectra of I and 4-methyl-2,6-dibenzoylphenol (mdbpH) also predicted by the B3LYP/6-31g(d) method show some blue shifts compared with their experimental data. There are significant changes in corresponding bond lengths and angles and crystal packing of phenol-based diketones having OH, CH3 or C(CH3)3 substituents in the para-position. Density functional theory (DFT) molecular orbital calculations have reproduced the structures of 4-methyl-2,6-dibenzoylphenol (mdbpH) and 4-tert-butyl-2,6-dibenzoylphenol (bdbpH, I) on the whole. The electronic spectra predicted by DFT MO calculations show some blue shifts compared with their experimental data.

Solid-State Photocycloaddition Reactions of Tri-2-Pyrones with Benzophenone

Solid-state photocycloaddition reactions between tri-2-pyrones (1a,1b) with benzophenone (2) gave the corresponding oxetane derivatives (3a:3a′=1:1 and 3b:3b′=1:1, 1:2 adducts) with high site- and regioselectivity across the C5-C6 , C5′-C6′ and C5′′-C6′′ double bonds in 1 via the triplet excited state of 2. The site- and regioselectivities were explained by MO calculations. The hydrogen-bonding interaction between 2 and 1a, 1b and the triplet reaction mechanism were also explained by the IR analyses and the quenching experiments, respectively.

W4Br10 Cluster Intermediates in the Solid State Nucleation of W6Br12

AbstractThe new adduct W4Br10·2SbBr3 and the new binary compound W4Br10 were obtained as products in a reaction cascade in which WBr6 was reacted with elemental antimony at successively increased temperatures. The crystal structures of both compounds were refined from X‐ray powder diffraction data and their electronic structures were analyzed by MO calculations. The cluster compounds W4Br10·2SbBr3 and W4Br10 appear as intermediates in the solid state nucleation of W6Br12. The overall reaction cascade involves tungsten clusters having tetrahedral (W4), square pyramidal (W5) and finally octahedral (W6) cluster cores.

What Controls the Magnetic Interaction in bis‐μ‐Alkoxo MnIII Dimers? A Combined Experimental and Theoretical Exploration

The synthesis and magnetic characterisation of a series of bis-μ-alkoxide bridged Mn(III) dinuclear complexes of general formula [Mn(III)(2)(μ-OR)(2)(biphen)(2)(ROH)(x)(L)(y)] (where R = Me, Et; H(2) biphen = 2,2'-biphenol and L = terminally bonded N-donor ligand) is described, doubling the literature basis set for this type of complex. Building on these findings we have categorised all known μ-OR bridged Mn(III) dinuclear complexes into one of three classifications with respect to their molecular structures. We have then employed DFT and MO calculations to assess all potential magneto-structural correlations for this class of compound in order to identify the structural requirements for constructing ferromagnetic family members. Our analysis indicates that the most influential parameter which governs the exchange interaction in this class of compounds is the relative orientation of the JT axes of the Mn(III) atoms. A perpendicular orientation of the JT axes leads to a large ferromagnetic contribution to the exchange. These results also suggest that a large ferromagnetic interaction and a large anisotropy are unlikely to co-exist in such structural types.

Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic – monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.

Efficient evaluation of Coulomb integrals in a mixed Gaussian and plane-wave basis using the density fitting and Cholesky decomposition

The objective of this paper is to show that the density fitting (resolution of the identity approximation) can also be applied to Coulomb integrals of the type (k(1)(1)k(2)(1)|g(1)(2)g(2)(2)), where k and g symbols refer to plane-wave functions and gaussians, respectively. We have shown how to achieve the accuracy of these integrals that is needed in wave-function MO and density functional theory-type calculations using mixed Gaussian and plane-wave basis sets. The crucial issues for achieving such a high accuracy are application of constraints for conservation of the number electrons and components of the dipole moment, optimization of the auxiliary basis set, and elimination of round-off errors in the matrix inversion.

The impact of igneous bedrock weathering on the Mo isotopic composition of stream waters: Natural samples and laboratory experiments

River waters have been shown to be systematically enriched in the heavy molybdenum (Mo) isotopes when compared to typical granites and basalts, which generally possess Mo isotopic compositions (δ98/95Mo) of around 0‰. This inconsistency has been used to argue against weathering of crustal rocks as the cause for heavy riverine δ98/95Mo signatures. Incongruent dissolution of primary bedrock, however, may be an important process by which the anomalous Mo signatures of the river dissolved load are produced. This study therefore investigates the effect of igneous crustal rock weathering on the aquatic δ98/95Mo signal by comparing stream water and bedrock Mo isotope data to results of bulk rock leach experiments. For this purpose, stream water and bedrock (orthogneiss, granite, basalt), as well as soil and vegetation samples were collected in a small catchment in the French Massif Central. In accordance with the results of earlier studies on riverine Mo, both streams are isotopically heavier (δ98/95Mo=0.5–1.1‰) than the typical granites and basalts. The excellent agreement of these data with those of Mo released during experimental leaching of the basalt bedrock (0.6–1.0‰) identifies a predominance of basalt weathering over the stream water Mo geochemistry, while other processes (i.e. soil formation, secondary mineral precipitation and adsorption) are subordinate in this catchment. Given that the basalt bulk rock δ98/95Mo reflects a value typical for crustal magmatic rocks (ca. 0.1‰), Mo isotope fractionation during the incongruent dissolution of basalt can explain the observed isotopically heavy aquatic Mo signatures. Laser ablation analyses demonstrate that the volumetrically minor magmatic sulfides can be highly enriched in Mo and mass balance calculations identify the sulfide melt inclusions as the principal Mo source for the leach solutions. These data suggest that the magmatic sulfides possess a distinctly heavier δ98/95Mo signature than the coexisting silicate melt. In this case, Mo would behave like Fe by showing a detectable isotope fractionation at magmatic temperatures. Incongruent crustal bedrock weathering may thus cause a preferential release of heavy Mo isotopes. This effect, however, is highly dependent on the primary bedrock mineralogy. Consequently, the average continental runoff may have been significantly affected by incongruent weathering during periods when the Earth system was exceptionally far from steady state, e.g., large glaciations with enhanced physical weathering or large subaerial basalt eruptions such as the Deccan and the Siberian plateau.

The CH/π hydrogen bond: Implication in chemistry

Abstract The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

Basis set dependence of molecular information channels and their entropic bond descriptors

Information channels from SCF MO calculations using different basis sets and their entropic bond descriptors are compared within the orbital communication theory. In this information-theoretic (IT) treatment of communications between basis functions the overall covalency and ionicity bond components reflect the average communication noise and information flow, respectively, in the resolution level specified by the adopted set of basis functions. The basis-set dependence of the orbital conditional probabilities and their entropic descriptors of the information covalency/ionicity content is explored. Compared to the minimum set \({{\bf \chi}}\) of the occupied atomic orbitals of the separated constituent atoms, the extended basis sets of Gaussian orbitals and/or their formal contractions generally give rise to a higher IT-covalency and lower IT-ionicity descriptors of the system chemical bonds. In the augmented set case, \({{\bf \chi}^{aug.} = ({\bf \chi},{\bf \psi})}\) , containing the polarization function complement \({{\bf \psi}}\) of \({{\bf \chi}}\) , the use of only \({{\bf \chi} \rightarrow {\bf \chi}}\) communications is advocated in a semi-quantitative chemical interpretation of the IT bond indices. The maximum-overlap criterion is used to transform the general (orthonormal) extended basis \({{\bf \xi}}\) to its semi-augmented form \({\widetilde{\bf \chi}^{aug.} = \widetilde{\bf \xi}=(\widetilde{\bf \chi}, \widetilde{\bf \psi}),}\) in which \({\widetilde {\bf \chi} \approx {\bf \chi}}\) and \({\widetilde {\bf \psi} \approx{\bf \psi}}\), which facilitates the near minimum basis set interpretation of bond descriptors and extraction of communications involving the polarization functions \({{\widetilde {\mathbf \psi}}}\) . A similar transformation using the minimum information distance criterion can be also envisaged. The effect of the atomic reduction of the molecular channels, which misses the effect of the “internal” communications (bonds) on constituent atoms, is also examined. As intuitively expected, the IT descriptors of such reduced channels are found to be less sensitive to the basis set enlargement.

EPR Spectra and Spin Density Distribution of O,S-Dimethyl 4,4-Dithioterephthalate Radical Anions

The preparation of O-methyl S-trideuteromethyl 4,4-dithioterephthalate and S-methyl O-trideuteromethyl 4,4-dithioterephthalate is described. The EPR spectra of the corresponding radical anions are measured. Comparison with the spectrum of O,S-dimethyl 4,4-dithioterephthalate radical anions allows the unequivocal assignment of the proton hyperfine structure (proton “hfs”) coupling constants in the above asymmetric species. Assignment of the arene proton hfs coupling constants is achieved by PM6 and density functional theory MO calculations of the spin density distribution and application of McConnell's relationship aH μ = −2.4·ρπ μ. The spin density distribution in the asymmetric title compound is compared with those in the radical anions of dimethyl terephthalate and the corresponding symmetric sulfur analogs.

Experimental and Theoretical Studies on Organic D‐π‐A Systems Containing Three‐Coordinate Boron Moieties as both π‐Donor and π‐Acceptor

Four linear π-conjugated systems with 1,3-diethyl-1,3,2-benzodiazaborolyl [C(6)H(4)(NEt)(2)B] as a π-donor at one end and dimesitylboryl (BMes(2)) as a π-acceptor at the other end were synthesized. These unusual push-pull systems contain phenylene (-1,4-C(6)H(4)-; 1), biphenylene (-4,4'-(1,1'-C(6)H(4))(2)-; 2), thiophene (-2,5-C(4)H(2)S-; 3), and dithiophene (-5,5'-(2,2'-C(4)H(2)S)(2)-; 4) as π-conjugated bridges and different types of three-coordinate boron moieties serving as both π-donor and π-acceptor. Molecular structures of 2, 3, and 4 were determined by single-crystal X-ray diffraction. Photophysical studies on these systems reveal blue-green fluorescence in all compounds. The Stokes shifts for 1, 2, and 3 are notably large at 7820-9760 cm(-1) in THF and 5430-6210 cm(-1) in cyclohexane, whereas the Stokes shift for 4 is significantly smaller at 5510 cm(-1) in THF and 2450 cm(-1) in cyclohexane. Calculations on model systems 1'-4' show the HOMO to be mainly diazaborolyl in character and the LUMO to be dominated by the empty p orbital at the boron atom of the BMes(2) group. However, there are considerable dithiophene bridge contributions to both orbitals in 4'. From the experimental data and MO calculations, the π-electron-donating strength of the 1,3-diethyl-1,3,2-benzodiazaborolyl group was found to lie between that of methoxy and dimethylamino groups. TD-DFT calculations on 1'-4', using B3LYP and CAM-B3LYP functionals, provide insight into the absorption and emission processes. B3LYP predicts that both the absorption and emission processes have strong charge-transfer character. CAM-B3LYP which, unlike B3LYP, contains the physics necessary to describe charge-transfer excitations, predicts only a limited amount of charge transfer upon absorption, but somewhat more upon emission. The excited-state (S(1)) geometries show the borolyl group to be significantly altered compared to the ground-state (S(0)) geometries. This borolyl group reorganization in the excited state is believed to be responsible for the large Stokes shifts in organic systems containing benzodiazaborolyl groups in these and related compounds.

Development of the four-body corrected fragment molecular orbital (FMO4) method

The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller–Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework.

ChemInform Abstract: Exploration of Novel Medicinal Leads by Use of Natural Products Inhibiting Nuclear Export of Proteins as Scaffolds

AbstractReview: 40 refs.