DFT Molecular Orbital Calculations Research Articles

Computational study of hybrid chalcogenoborate anions

DFT and MP2 molecular orbital (MO) calculations were used to establish the structural and stability relationships for different members of chalcogenoborate anions within the following series: BSe x S 3 - x 3 - ( x = 0–3), B 2 Se x S 4 - x 2 - ( x = 0–4), B 2 Se x S 5 - x 2 - ( x = 0–5), and B 3 Se x S 6 - x 3 - ( x = 0–6). Full geometry optimization for each anion was performed at the PBE0 and MP2(full) levels of theory using the 6-311+G(2d) basis set. Molecular local minima for all species were confirmed by fundamental vibration calculations which have shown no imaginary vibrations. All anions adopt planar geometry. Clear similarity between the trends in different bond types and experimental results is observed. Relative stabilities of the anions have been calculated at the PBE0 and MP2 levels of theory and indicate that the stability of the anions within each series decreases with increasing selenium content. AIM and ELF analyses were used to probe the bonding in the B 2 E 5 2 - anions.

Dinuclear Rh(I) complex with 2,7-bis(diphenylphosphino)-1,8-naphthyridine: Synthesis, structure, and dynamic property

Reaction of [RhCl(cod)] 2 with 2,7-bis(diphenylphosphino)-1,8-naphthyridine (dpnapy) and 2,6-xylyl isocyanide (XylNC) in the presence of NH 4PF 6 afforded the dirhodium(I) complex, [Rh 2(μ-dpnapy) 2(XylNC) 4](PF 6) 2 ( 5), and similar procedures using [MCl 2(cod)] (M = Pt, Pd) resulted in the formation of [Pt 2(μ-dpnapy) 2(XylNC) 4](PF 6) 4 ( 6) and [Pd 2Cl 2(μ-dpnapy) 2(XylNC) 2](PF 6) 2 ( 7). Complexes 5– 7 were characterized by elemental analysis, IR, UV–Vis, 1H and 31P{ 1H} NMR, and ESI mass spectroscopic techniques, to involve a small and rigid d 8 {M 2(μ-dpnapy) 2} metallomacrocycle. Complex 5 readily incorporated a silver(I) ion into the macrocycle to afford [Rh 2Ag(μ-dpnapy) 2(XylNC) 4](PF 6) 3 ( 8) which was characterized by X-ray crystallography. The Ag(I) ion is trapped by two trans N atoms of dpnapy ligands, resulting in an asymmetric Rh–Ag⋯Rh structure, determined as a disordered model in the crystal structure, and however, in a CH 2Cl 2 solution, a dynamic interconversion of the two Ag-trapped sites was observed with low-temperature NMR studies, which was further supported by DFT molecular orbital calculations. When an acetonitrile solution of complex 5 was treated over a droplet of mercury(0), the polymeric compound formulated as {[Rh(μ-dpnapy)(XylNC) 2](PF 6)} n ( 9) was isolated as yellow single crystals, which were revealed by X-ray crystallography to consist of C 6 helical rods along c axis with a pitch of 33.5 Å (rise of unit = 5.6 Å) and a diameter of 20.64 Å.

Experimental and calculated circular dichroism spectra of monoaza[5]helicenes

Circular dichroism (CD) spectra have been measured in the range of 400–200 nm on CH 3OH solutions of both enantiomers for the almost complete series of monoaza[5]helicenes, namely the molecules where the hetero N atom occupies positions 1, 3, 4, 5, 6, and 7, respectively (the 2 isomer is missing due to difficulties in the synthesis). CD spectra recorded at controlled room temperature allow one to define precise racemization rates, that are nicely interpreted on the basis of DFT molecular orbital calculations. Time-dependent DFT methods provide us with calculated CD and UV spectra, that are compared with the corresponding experimental data. We discuss the role of the N atom in determining the height of the racemization barrier and in shaping the appearance of the CD spectra.

Component analysis of the X-C-Y anomeric effect (X = O, S; Y = F, OMe, NHMe) by DFT molecular orbital calculations and natural bond orbital analysis

Six 2-Y-substituted oxacyclohexane and thiacyclohexane heterocycles (Y = F, OMe, NHMe) were examined using DFT molecular orbital calculations. Natural bond orbital (NBO) analysis of the total energy behaviour yielded the orbital-interaction factors contributing to the conformational equilibria. The dipole moments of the optimized systems were used to estimate the electrostatic contributions to the anomeric effect. The primary determinant of the X-C-Y anomeric effect was found to be the orbital interaction components associated with the combined endo- and exo-anomeric effects acting in concert in the axial conformers. Electrostatic interactions made a contribution to the observed conformer stabilization in all cases, but did not account for the relative magnitudes of the energy differences among conformers of homologous molecules. In the case of the methylamino substituent, accentuated steric interactions in the axial conformer precluded stabilization by the exo-anomeric interaction and consequently, the net endo/exo anomeric stabilization did not dominate the conformational equilibria.Key words: anomeric effect, component analysis, natural bond orbital analysis, electrostatic, steric, and orbital interaction effects.

The chemical reactivity of some terpenes investigated by alumina catalyzed epoxidation with hydrogen peroxide and by DFT calculations

The selectivity of the alumina catalyzed epoxidation of (S)-limonene, citronelal, citral, citronelol and (1S)-(α)-pinene with aqueous 70wt% and anhydrous 24wt% hydrogen peroxide is described. DFT molecular orbital calculations were used aiming at a better understanding of the reactivity of these terpenes. The more nucleophilic carbon–carbon double bond, which has a higher molecular orbital energy, is preferentially epoxidized (site-selectivity). Furthermore, a preference for epoxidation in competition with other possible reactions is observed for citronelal, citral, citronelol and (1S)-(α)-pinene (chemo-selectivity). Nonetheless, we were not able to achieve a stereo-selective epoxidation of the terpenes using alumina and hydrogen peroxide.

Synthesis and Structural Analysis of 3,6,8,11,16-Hexahydrodicyclopenta[c,h][1,6]dithiecin

The cycloaddition reaction of 3,6,9-trihydrocyclohepta[c][1,2]dithiin (5), prepared from 3,4-bis(bromomethyl)-1,3,5-cycloheptatriene (3) in two steps, with 3,4-dimethylene-l,5-cycloheptadiene (6) in the presence of boron trifluoride-etherate gave 3,6,8,11,16-hexahydrodicyclohepta[c,h][1,6]dithiecin (2). The temperature-dependent NMR study indicated that 2 possesses the fluxional tetrahydrodithiecin moiety in solution at room temperature. The X-Ray crystal structure analysis showed that 2 has an S-letter shape which was supported as the most stable conformer by DFT molecular orbital calculations.

Synthetic Applications of (Me3SiNSN)2E (E: S, Se) in Chalcogen‐Nitrogen Chemistry: Formation and Structural Characterization of Cl2TeESN2 (E: S, Se) and [PPh4]2 [Pd2(μ‐Se2N2S)X4] (X: Cl, Br).

AbstractFor Abstract see ChemInform Abstract in Full Text.

An ab initio and DFT comparative study of electronic effects on spin multiplicities and structures of X–C 2N carbenes

Ab initio and DFT molecular orbital calculations are used to determine singlet–triplet energy splits, Δ E s–t,X, as well as relative energies, in the carbenic reactive intermediates X–C 2N, at seven levels of theory: B3LYP/6-31G*, MP2/6-31G*, B3LYP/6-311++G**, MP2/6-311+G*, MP3/6-311G*, MP4(SDTQ)/6-311++G** and QCISD(T)/6-311++G**; for X=H, NH 2, CN and OMe. MP3 results are more consistent to the B3LYP and/or QCISD(T) rather than the MP2 or MP4 results. Three possible structures considered for each singlet (s) and/or triplet (t) carbenes are: 3-X-2-azacyclopropenylidene ( 1 s-X and 1 t-X), [(X-imino)methylene]carbene ( 2 s-X and 2 t-X), and X-cyanocarbene ( 3 s-X and 3 t-X). Species 1 t-H, 1 t-NH2, 1 t-OMe, 2 t-NH2, 3 t-NH2, 3 s-OMe and 3 t-OMe show imaginary frequencies, so their corresponding structures are not minima and appear as transition states on the potential energy surface of X–C 2N. Cyclic triplet 1 t-CN, upon optimization transforms to an acyclic carbenonitrene structure. For all X–C 2N species inspected, Δ E s–t,X appears the highest for X=NH 2, and the lowest for X=H. For the six H–C 2N species with X=H, the order of relative energy is: 1 t-H> 2 s-H> 2 t-H> 3 s-H> 1 s-H> 3 t-H. Likewise, for the six structures with X=CN, the order of relative energy is: 1 t-CN> 2 s-CN> 2 t-CN> 1 s-CN> 3 s-CN> 3 t-CN. Finally, the order of relative energy for 12 structures with X=NH 2 and/or OMe is: 2 t-X> 1 t-X> 2 s-X> 3 t-X> 1 s-X> 3 s-X. The lowest energy minima, among the 12 species with X=H and/or CN, are triplet 3 t-X; while the lowest energy minimum, among the six species with X=NH 2 is singlet 3 s-NH2. The discussion includes geometrical parameters, dipole moments, charges and bond orders of 1– 3.

Synthetic Applications of (Me3SiNSN)2E (E = S, Se) in Chalcogen-Nitrogen Chemistry: Formation and Structural Characterization of Cl2TeESN2(E = S, Se) and [PPh4]2[Pd2(μ-Se2N2S)X4] (X = Cl, Br)

The reaction of (Me3SiNSN)2S with TeCl4 in CH2Cl2 affords Cl2TeS2N2 (1) and that of (Me3SiNSN)2Se with TeCl4 produces Cl2TeSeSN2 (2) in good yields. The products were characterized by X-ray crystallography, as well as by NMR and vibrational spectroscopy and EI mass spectrometry. The Raman spectra were assigned by utilizing DFT molecular orbital calculations. The pathway of the formation of five-membered Cl2TeESN2 rings by the reactions of (Me3SiNSN)2E with TeCl4 (E = S, Se) is discussed. The reaction of (Me3SiNSN)2Se with [PPh4]2[Pd2X6] yields [PPh4]2[Pd2(mu-Se2N2S)X4] (X = Cl, 4a; Br, 4b), the first examples of complexes of the (Se2N2S)2- ligand. In both cases, this ligand bridges the two palladium centers through the selenium atoms.

Interconverting WW Triple Bonds and W4 Clusters: Structures of W4(OPrn)16 and [Li2W2(OPrn)8(DME)]2*

Alcoholysis of W2(NMe2)6 with excess n-propanol in hexane yields the tetranuclear cluster, W4(OPrn, I. Reduction of I with two equivalents of Li2COT in THF gives a small yield of Li2W2(OPrn)8. Single crystals were isolated by cooling the product mixture in DME and were shown to be [Li2W2(OPrn)8(DME)]2, II, which consists of a unique “dimer of dimers” structure. In this reaction sequence, W416+ cluster formation is followed by four electron reduction to reform the (W≡W)6+ unit. Better yields of the lithium salt can be obtained by the addition of LiOPrn/HOPrn solutions to W2(OBut)6 in which case Li2W2(OPrn)8 has been obtained as a 1:1 adduct with LiOPr. This identity of this salt was confirmed by solution NMR spectroscopy. In the alternative reaction, the (W≡W)6+ center remains intact from reactant to product. No attempt has been made to separate the product from excess LiOPr. DFT (ADF 2004.01) molecular orbital calculations on the model cluster W4(OH)16 are used to help elucidate the disruption of the W4 cluster upon four electron reduction. The molecular structures of compounds I and II are reported.

DFT and ab initio direct dynamics study on the reaction of H 2 loss reaction from H 2BNH 2

DFT and ab initio molecular orbital calculations are carried out for the H 2 loss reaction from aminoborane (H 2BNH 2). The geometries of all the stationary points are optimized at the B3LYP and MP2 methods with a series of basis sets up to aug-cc-pVTZ. The harmonic vibrational frequencies are calculated at the same level of theory. One transition state is found at the B3LYP/(aug-)cc-pVTZ and MP2/(aug-)cc-pVTZ level of theory. The energies and enthalpies are refined at the G3, G3MP2, G3MP2B3, CBS-Q, CBS-QB3, and HL methods based on the geometries optimized using B3LYP/aug-cc-pVTZ method. The rate constants are evaluated using the conventional transition-state theory (TST), canonical variational transition-state theory (CVT), and canonical variational transition-state theory with small curvature tunneling correction (CVT/SCT) and conventional transition-state theory with Eckart tunneling correction (TST/Eckart).

A study of 2-azido-3,5-dichlorobiphenyl by nano- and picosecond laser flash photolysis and computational methods

The dynamics of singlet 3,5-dichloro-2-biphenylnitrene and the products of its rearrangement were monitored by pico- and nanosecond laser flash photolysis and the results were consistent with the predictions of DFT and ab initio molecular orbital calculations.

Kinetics and Mechanisms for the Reactions of Phenyl Radical with Ketene and its Deuterated Isotopomer: An Experimental and Theoretical Study

Kinetics and mechanism for the reaction of phenyl radical (C6H5) with ketene (H2C beta=C alpha=O) were studied by the cavity ring-down spectrometric (CRDS) technique and hybrid DFT and ab initio molecular orbital calculations. The C6H5 transition at 504.8 nm was used to detect the consumption of the phenyl radical in the reaction. The absolute overall rate constants measured, including those for the reaction with CD2CO, can be expressed by the Arrhenius equation k = (5.9 +/- 1.8) x 10(11) exp[-(1160 +/- 100)/T] cm3 mol-1 s-1 over a temperature range of 301-474 K. The absence of a kinetic isotope effect suggests that direct hydrogen abstraction forming benzene and ketenyl radical is kinetically less favorable, in good agreement with the results of quantum chemical calculations at the G2MS//B3LYP6-31G(d) level of theory for all accessible product channels, including the above abstraction and additions to the C alpha, C beta, and O sites. For application to combustion, the rate constants were extrapolated over the temperature range of 298-2500 K under atmospheric pressure by using the predicted transition-state parameters and the adjusted entrance reaction barriers E alpha = E beta = 1.2 kcal mol-1; they can be represented by the following expression in units of cm3 mol-1 s-1: k alpha = 6.2 x 10(19)T-23 exp[-7590/T] and k beta = 3.2 x 10(4)T2.4 exp[-246/T].

Cyclizative radical carbonylations of azaenynes by TTMSS and hexanethiol leading to alpha-silyl- and thiomethylene lactams. Insights into the E/Z stereoselectivities.

Free-radical mediated cyclizative carbonylations of azaenynes were carried out using TTMSS as a radical mediator to compare the efficiency and the stereochemistry with those using tributyltin hydride. Using a substrate concentration of 0.1 M, the reactions gave good yields of alpha-silylmethylene lactams having four to seven-membered rings. The observed E-diastereoselectivity of the resulting vinylsilane moiety is in sharp contrast to the Z-selectivity observed during the analogous carbonylation using tributyltin hydride. When hexanethiol was used as the radical mediator, alpha-thiomethylene lactams were formed with E-favoring stereoselectivity again. Ab initio and DFT molecular orbital calculations on the stability of E and Z products were carried out for a set of five-membered methylene lactams bearing SnH3, SiH3, and SMe groups. The distinct thermodynamic preference for the Z-isomer was only predicted for the Sn-bearing lactam. A steric effect due to the bulky (TMS)3Si group is proposed for the E-selectivity observed in the TTMSS-mediated reaction.

Electronic Interactions in (η6-Arene) Ferracarboranes1

The electronic structures of a series of di- and trinuclear ferracarboranes that incorporate FeC2B4 cluster units connected by aryl, heterocyclic, or alkynyl bridges or via direct intercluster B−B bonding have been explored by cyclic voltammetry, controlled-potential coulometry, and DFT and PM3 molecular orbital calculations. The data reflect the strong electron-donating properties of the Et2C2B4H42- carborane ligand; thus, in the ferrocenyl derivative (η6-C6H6)Fe(Et2C2B4H3-5-Fc) there is a substantial flow of electron density from the ferracarborane cluster to the ferrocenyl moiety. In all complexes examined, one or more reversible oxidations of FeII to FeIII centers were observed, with varying degrees of separation of successive E° values, indicating a range of electron-delocalization behavior. In many of the observed mixed-valent FeII−FeIII species the evidence suggests little or no metal−metal communication, paralleling earlier studies of small arene-ferracarboranes; however, significant delocalizatio...

Theoretical Study of Chloroalkenylperoxy Radicals

DFT and ab initio molecular orbital calculations have been performed to investigate the structures and energetics of the Cl−O2−isoprene peroxy radicals arising from the Cl-initiated oxidation of is...

Experimental and theoretical studies on ferromagnetically coupled metal complexes with imino nitroxides.

Copper(II), zinc(II), and nickel(II) complexes with tridentate imino nitroxyl diradicals, [CuCl(bisimpy)(MeOH)](PF(6)) (1), [ZnCl(2)(bisimpy)] (2), and [NiCl(bisimpy)(H(2)O)(2)]Cl x 2H(2)O (3) (bisimpy = 2,6-bis(1'-oxyl-4',4',5',5'-tetramethyl-4',5'-dihydro-1'H-imidazol-2'-yl)pyridine), were prepared, and their magnetic properties were studied. In 1, the Cu(II) ion has a square pyramidal coordination geometry, of which the equatorial coordination sites are occupied by three nitrogen atoms from the bisimpy and a chloride ion. The coordination geometry of the Zn(II) ion in 2 can be described as a trigonal bipyramid, with two chloride ions and a bisimpy. In 3, the Ni(II) ion has a distorted octahedral coordination geometry, of which four coordination sites are coordinated by the bisimpy and chloride ion, and two water molecules occupy the remaining cis positions. Magnetic susceptibility and EPR measurements revealed that in 1 and 3 the Cu(II) and Ni(II) ions with imino nitroxyl diradicals were ferromagnetically coupled, with the coupling constants J (H = -2J(ij) summation operator S(i)S(j)) of +165(1) and 109(2) cm(-1), respectively, and the intraligand ferromagnetic interactions in 1-3 were very weak. DFT molecular orbital calculations were performed on the diradical ligand, 1, and 2 to study the spin density distribution before and after coordination to the metal ions.

Pyrazole N‐methylide radical cation: ion–molecule reactions in a new hybrid tandem mass spectrometer and DFT molecular orbital calculations

Pyrazole N‐methylide radical cation: ion–molecule reactions in a new hybrid tandem mass spectrometer and DFT molecular orbital calculations

PyrazoleN-methylide radical cation: ion-molecule reactions in a new hybrid tandem mass spectrometer and DFT molecular orbital calculations

PyrazoleN-methylide radical cation: ion-molecule reactions in a new hybrid tandem mass spectrometer and DFT molecular orbital calculations

Electron-deficient triruthenium and triosmium clusters from the reaction of the cluster anions [HM 3(CO) 11] − (M=Ru, Os) with tricyclohexylphosphine in methanol

The reaction of Na[HRu 3(CO) 11] with an excess of tricyclohexylphosphine in methanol gives the neutral complex H 2Ru 3(CO) 6(PCy 3) 3 which is the first 44 e − triruthenium cluster reported. This highly electron-deficient species reacts with carbon monoxide to give the saturated 48 e − cluster Ru 3(CO) 9(PCy 3) 3. The electronic structure of the novel 44 e − cluster was established by EHT and DFT molecular orbital calculations of isoelectronic model compounds. The analogous reaction of [N(PPh 3) 2][HOs 3(CO) 11] with PCy 3 in methanol affords the 46 e − cluster H 2Os 3(CO) 7(PCy 3) 3, the first trisubstituted derivative of H 2Os 3(CO) 10. In all cases methanol acts as source of protons for the formation of the hydrido clusters.