Pseudorotation Pathway Research Articles

Surface Pseudorotation in Lewis-Base-Catalyzed Atomic Layer Deposition of SiO2: Static Transition State Search and Born–Oppenheimer Molecular Dynamics Simulation

Atomic layer deposition (ALD) is a novel deposition technique for constructing uniform, conformal, and ultrathin films in microelectronics, catalysis, energy storage, and conversion. The possible reaction pathways for the uncatalyzed and catalyzed ALD of silicon dioxide (SiO2) using SiCl4 and H2O have been investigated by density functional theory (DFT) calculations, combining static transition state searches with Born–Oppenheimer molecular dynamics (BOMD) simulations. In stepwise pathways of the uncatalyzed SiO2 ALD reaction, the rate-determining step is the Si–O bond formation accompanied by the rotation of SiCl4 with the activation free energy of 23.8 kcal/mol. The introduction of Lewis-base catalyst, pyridine or NH3, can reduce the activation free energy to 6.8 or 2.7 kcal/mol. The low energy barrier and flexible pentacoordinated intermediate facilitate the surface pseudorotation (SPR) pathway, which is similar to Berry pseudorotation (BPR) pathway of the trigonal bipyramid (TBP) molecules, such as Fe...

2,6-Bis(p-tolyliminomethyl)pyridine-κ3N,N′,N′′]dichloridocopper(II)

The title compound, [CuCl2(C21H19N3)], lies on a twofold rotation axis that passes through the Npyrid­yl—Cu bond; this symmetry element relates one half of the organic ligand to the other as well as one Cl ligand to the other. The three N atoms span the axial–equatorial–axial sites of the trigonal-bipyramidal coordination polyhedron; the geometry of the CuII atom is 31% distorted from trigonal-bipyramidal (towards square-pyramidal along the Berry pseudorotation pathway).

2,6-Bis(6-methylquinolin-2-yl)pyridine-κ3N,N′,N′′]dichloridomanganese(II)

In the mol­ecule of the title compound, [MnCl2(C25H19N3)], the three N atoms span the axial–equatorial–axial sites of the trigonal-bipyramidal coordination polyhedron; the geometry of the MnII atom is 34% distorted from trigonal-bipyramidal (towards square-pyramidal along the Berry pseudorotation pathway). One of the Cl atoms is disordered over two positions in a 0.82 (3):0.18 (3) ratio. Weak inter­molecular C—H⋯Cl hydrogen bonding occurs in the crystal structure.

2,6-Bis(6-methylquinolin-2-yl)pyridine-κ3N,N′,N′′]dichloridoiron(II)

In the mol­ecule of the title compound, [FeCl2(C25H19N3)], the three N atoms span the axial–equatorial–axial sites of the trigonal-bipyramidal coordination polyhedron; the geometry of the FeII atom is 32% distorted from trigonal-bipyramidal (towards square-pyramidal along the Berry pseudorotation pathway). One of the Cl atoms is disordered over two positions in a 0.938 (11):0.062 (11) ratio. Inter­molecular C—H⋯Cl hydrogen bonding occurs in the crystal structure.

Four independent structures of a pentacoordinate silicon species at different points on the Berry pseudorotation pathway

A new pentacoordinate silicon species containing two chelating ligands has been synthesized. The structures of four independent cations of the same compound correspond to different points on the Berry pseudorotation pathway. The percentage of square planar character varies between 19% and 40%.

Chlorido(pentane-2,4-dionato-κ2O,O′)(1,10-phenanthroline-κ2N,N′)copper(II)

The CuII atom in the title compound, [Cu(C5H7O2)Cl(C12H8N2)], shows a distorted square-planar coordination; the chelating N and O atoms occupy the basal sites and the Cl atom the apical site. The square-pyramidal character along the Berry D 3h–C 4v pseudorotation pathway is 92%.

Solid state conformational preferences in transition metal complexes double bridged by phosphate and related ligands

The conformational preferences in the {M(μ-OPO)} 2 core of transition metal complexes double bridged by phosphate and related ligands have been determined using data retrieved from the Cambridge Structural Database by a probabilistic method. The preferred conformations lie on a pseudorotation pathway ( chair and twist-chair conformations). The influence of intra-ring bridges, metal atom, coordination number or ligand in the conformational preferences has been investigated.

Theoretical ab initio study of Xenon pentafluoride anion. Mechanism of Xenon pseudorotation

Ab initio calculations have been performed on XeF 5 − anion at the MP2 and CCSD(T) levels with a large basis set. Four extrema have been optimized and characterized by frequencies analysis. We find the absolute minimum to be of D 5h symmetry in accordance with the experimental data; the theoretical vibrational spectrum of this minimum is in good agreement with the experimental one. Three other extrema are found to be higher in energy depending on the angular separation of the Xenon lone pairs as predicted by the VSEPR theory. Finally the characterized transition state has been found to belong to the Xenon pseudorotation pathway.

Principal component analysis of conformations in fused ring chelate complexes: conformer identification, stereochemistry, and interconversion pathways

Data were retrieved from the Cambridge Structural Database for crystal structures containing metal complexes of ethylenediamine (en), tetramethylethylenediamine (tmeda), bis(dimethylphosphino)ethane (dmpe), bis(diphenylphosphino)ethane (dppe) chelate complexes [M(en) (279 structures, 468 fragments), M(tmeda) (156 structures, 181 fragments), M(dmpe) (205 structures, 288 fragments) and M(dppe) (273 structures, 338 fragments)] and fused five-membered chelate ring systems [complexes of diethylenetriamine, M(dien) (91 structures, 108 fragments), tris(2-aminoethyl)amine, M(nn3) (49 structures, 54 fragments), tris(2-diphenylphosphinoethyl)phosphine, M(pp3), and tris(2-diphenylphosphinoethyl)amine, M(np3) (54 structures, 56 fragments)], and have been analysed using principal component analysis (PCA) of the intra-ring torsion angles. A limited number of preferred conformers is observed for each system: enantiomeric twist conformations (δ or λ) for M(en), M(tmeda), M(dppe) and M(dmpe); three unique conformers: δδ (and its enantiomer λλ), λδ or δλ for M(dien); and two types for M(nn3) or M(xp3) (x = n or p): two enantiomeric C3 symmetric A (λλλ, δδδ) and six equivalent B (δλδ, δδλ, λδδ, δλλ, λλδ, and λδλ) conformers of lower symmetry. The pseudorotation pathway for δ ↔ λ interconversion in the single ring systems is clear for M(dppe) and also for M(dmpe) but less so for M(en) and, M(tmeda). The δλ and λδ conformers of M(dien) apparently interconvert through δδ (or λλ) intermediates with one ring at a time inverting. Similarly the interconversion of conformers in the M(xp3) and M(nn3) systems seems likely, on the basis of the distribution of structures in conformation space, to follow a sequence δδδ ↔ δλδ ↔ λλδ ↔ λλλ (or its equivalent) but not δδδ ↔ δλδ ↔ δλλ ↔ λλλ. In the M(dien), M(nn3) and M(xp3) systems the conformation preferred is linked to the metal coordination geometry. In particular, the presence of an N–M–N angle approaching 180° in a mer-octahedral or square-based pyramid stereochemistry in M(dien) species enforces a δλ conformation. Similarly, related mer-like stereochemistry in M(nn3) and M(xp3) complexes leads to a B-type conformation. Longer M–N (or M–P) distances enforce more puckered, symmetrical, twist conformations of five-membered rings. A new pseudo-principal component analysis method is introduced which allows quantitative comparison of conformations in analogous but not identical ring systems. Conformations in M(en) are compared with M(dien) or M(nn3), with the single-ring system exhibiting less distorted conformations. Phosphine systems exhibit greater variation of conformation than their amine counterparts. In particular M(dmpe) systems show considerably more variation than M(tmeda) whereas M(dppe) species are more varied in conformation than are M(dmpe).

Conformational properties of cyclooctane: a molecular dynamics simulation study

Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400 K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied (313 and 400 K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boat-chair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.

Conformational properties of cyclooctane: a molecular dynamics simulation study

Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400 K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied (313 and 400 K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boat-chair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.

Pseudorotation pathway and equilibrium structure from the rotational spectrum of jet-cooled tetrahydrofuran

The rotational spectrum of jet-cooled tetrahydrofuran has been investigated in the 8–18 and 60–78 GHz frequency ranges. Only the four lowest vibrational levels remain populated in the jet conditions. Two pseudorotation vibrational spacings have been measured directly to be ΔE01=21 307.71(3) MHz and ΔE23=61 205.69(3) MHz. They have been used, together with the lowest 10 measured far infrared transition frequencies and with the effective moments of inertia of the ground state and their shifts upon excitation observed in this work, to determine the potential energy function for pseudorotation and the associated structural relaxations. The potential energy barriers are 45 cm−1 at the envelope conformation of the oxygen and 16 cm−1 at the twisted conformation of the Cβ–Cβ′ bond relative to the CαOCα′ plane. The four symmetrically equivalent equilibrium structures are close to the envelope conformations of the CH2 groups next to the oxygen atom. While the C–O bond lengths and the local CH2 angles appeared to remain unaffected by pseudorotation, significant changes found for the diagonal O⋯C distances as well as for the C–C and C–H bond lengths are of interest as possible effects of hyperconjugation.

1:1 Adducts of triphenyltin chloride with oxovanadium(IV) tetradentate Schiff-base complexes

Triphenyltin chloride– N, N′-ethylenebis(salicylideneiminato)oxovanadium(IV) (1/1), which crystallises from acetonitrile with half a molecule of the solvent, is a heterodinuclear entity that displays an almost linear tin–oxygen–vanadium unit [SnOV=172.7(2)°; SnO=2.382(2), VO=1.614(3) Å]. The tin atom shows approximately trigonal bipyramidal coordination in the adduct with the axial sites occupied by the O and Cl atoms. On the other hand, the vanadium atom is in square-pyramidal coordination, and the vanadium-containing moiety is 68% displaced along the Berry pseudorotation pathway from trigonal bipyramidal towards square pyramidal, compared with the 83% mean displacement for [VO(salen)] itself. The corresponding displacements for the vanadium moiety in Ph 3SnCl·VO(hap-1,2-pn)·2CH 3CN are 94% [SnO=2.405(6), VO=1.627(6) Å; SnOV=175.5(3)°] and 89% in Ph 3SnCl·VO[salen(3-OMe) 2]·CH 3CN [SnO=2.428(2), VO=1.625(2) Å; SnOV=167.5(1)°] [H 2hap-1,2-pn= N, N′-methylmethylenebis(2-phenolatoacetophenoneimine); H 2salen(3-OMe) 2= N, N′-ethylenebis(3-methoxysalicylideneimine)]. The [VO(salen)] adduct of N-triphenylstannyl-1,2-benzisothiazol-3(2 H)-one 1,1-dioxide has also been synthesised, and characterised by spectroscopic measurements.

Structures of Furanosides: Density Functional Calculations and High-Resolution X-ray and Neutron Diffraction Crystal Structures

Highly accurate and precise crystal structures of methyl R-D-arabinofuranoside, methyl ‚-D-ribofuranoside, methyl R-D-lyxofuranoside, and methyl R-D-xylofuranoside have been determined at 100 K by X-ray crystallography. The structures of methyl R-D-arabinofuranoside and methyl ‚-D-ribofuranoside have also been determined at 15 K by neutron diffraction. Equilibrium (re) geometries of the same compounds were computed by means of density functional methods using a variety of exchange-correlation functionals and a sequence of basis sets. The validity of the computed results was assessed by several criteria including agreement between computed and observed bond distances and bond angles, agreement between computed and observed ring conformations, and basis set convergence of the computed geometrical parameters. Particular reference was made to computed internal hydrogen bond parameters, which are especially sensitive to the quality of the theoretical treatment. Because of the intrinsic sensitivity of the conformation of the five-membered ring to bond lengths and bond angles, molecular mechanics and small basis set SCF treatments are wholly inadequate. Local density functional theory also fails because of a tendency to strongly underestimate internal hydrogen bond distances. When the B3LYP exchange-correlation functional is used, bond lengths and bond angles agree with the neutron diffraction values to within their experimental uncertainty and the ring conformation is qualitatively correct, as long as a basis set of at least double- œ plus polarization quality (such as cc-pVDZ) is used. Further expansion of the basis set leads to more accurate equilibrium bond lengths and bond angles but does not appreciably affect the ring conformation. For methyl R-D-arabinofuranoside, methyl ‚-D-ribofuranoside, and methyl R-D-xylofuranoside, there is very good correspondence between the best computed and observed ring conformations, even though some intermolecular hydrogen bonds in the crystal give way to internal hydrogen bonds in the predicted gas-phase structures. On the other hand, in the case of methyl R-D-lyxofuranoside, an O2H‚‚‚O4 internal hydrogen bond between the ring oxygen O4 and the hydroxyl hydrogen of a ring carbon (O2H) in the computed structure leads to a very large change of ring conformation from the northeast corner of the pseudorotation pathway (P ) 28°, crystal) to the southeast corner ( P ) 130°, computed).

Molecular structure and conformations of tetrahydrofurfuryl alcohol from a joint gas-phase electron diffraction and ab initio molecular orbital investigation

The molecular structure and conformational composition of tetrahydrofurfuryl alcohol in the gas-phase has been studied by a joint electron diffraction/ab initio method. The most abundant (84 ± 8%) conformer (A) in the gas-phase mixture was found to be stabilized by hydrogen bonding and had the OH group placed over the furanose ring, which had a distorted 4 T 3 conformation. The other conformer (B) with the relative abundance of 16 ± 8% had the OH group located outside the ring and directed toward the ring oxygen also participating in the hydrogen bond formation. The barrier heights to pseudorotation in different conformers were estimated from ab initio calculations. Torsion strain was found to contribute mainly to the higher barrier near the E 1 form of the ring due to considerable ring flattening. The flattening might be a consequence of unfavorable axial position of the substituent at that point along the pseudorotation pathway. Differences between parameters in the same conformers as well as differences between parameters in the various conformers were assumed in the electron diffraction structure analysis from the MP2( FC)/6–311++ G∗∗ ab initio calculations. The following values ( r g bond lengths and r a angles with total errors) were found for the main parameters in the most stable conformer: r( C− C) mean = 1.538 ± 0.004 A ̊ ; r( C- O) mean = 1.430 ± 0.003 A ̊ ; r( C- H) mean = 1.109 ± 0.003 A ̊ ; r( O- H) = 0.925 ± 0.012 A ̊ ; ∠ O 1− C 2−6 = 105.5 ± 1.4°; ∠ C 3− C 2− C 6 = 112.3 ± 0.8°; ∠ C 2− C 6− O 7 = 112.9 ± 1.0°; ∠ C 5− O 1− C 2 = 113.1 ± 1.6°; ∠ O 1− C 2− C 3 = 102.9 ± 0.6°; pseudorotation puckering amplitude q 0 = 9.8 ± 0.3°; pseudorotation phase angle f = 85.5 ± 6.4°.

Molecular structures of (tBu)Ga(S2CNnPr2)2 and (iPrO)Ga(S2CNEt2)2 : An example of an unusual ligand pseudorotation

The molecular structures of (tBu)Ga(S2CNnPr2)2 (1) and (iPrO)Ga(S2CNEt2)2 (2) have been determined. The variation in the geometries observed for bis-dithiocarbamate compounds of gallium, (X)Ga(S2CNMe2)2 (X=Cl, iPrO, tBu) do not lie along the Berry pseudorotation pathway for the square-based pyramid to trigonal bipyramid geometrical transition. Instead, the structures appear to lie on an unusual ligand two-step, “Texas,” pseudorotation mechanism which results in a highly distorted trigonal bipyramidal geometry. Crystal data: (1) monoclinic, P21,/c, a = 9.786(1), b = 29.218(3), c = 9.452(1) A, β = 108.379(9)°, V = 2564.7(5) A3, and Z = 4. (2) Monoclinic, P21/c, a = 10.980(3), b = 15.673(4), c = 12.461(3) A, β = 97.47(2)°, V = 2126.2(9) A3 and Z = 4.

Conformational equilibria of 2-substituted 1,3-dithio-5,6-benzocycloheptene and 1,3-dioxa-5,6-benzocycloheptene

The semiempirical PM3 method was used to study the Conformational equilibrium of the various chair, boat, twist and biplanar conformations of 1,3-dithio- and 1,3-dioxa-5,6-benzocycloheptene when groups having different dimensions substitute one or both of the hydrogen atoms at C 2. The results obtained show that bond lengths and bond angles are highly affected by the steric effect originating from the substituents. The chair conformation is the prevailing one in the 1,3-dithio-5,6-benzocycloheptene derivatives and the only possible when cumbersome substituents are attached at C 2, except in the di- t-butyl derivative. In the corresponding oxygenated molecules the chair form prevails when the steric effect is not relevant, otherwise the equilibrium shifts towards the twist conformation. The calculated barriers for the chair ↔ boat interconversion are in good agreement with the literature data concerning 1,3-dioxa-5,6-benzocycloheptene and its 2,2′-dimethyl derivative, whilst they are underestimated for the dithio derivatives. Barriers to the twist ↔ boat pseudorotation pathway are found only for some dithio derivatives. Ab initio 3G–21G ∗ calculations limited to the parent compounds were also performed.

Symmetry-modified conformational mapping and classification of the medium rings from crystallographic data. II. exo-unsaturated and heterocyclic seven-membered rings

Crystallographic results derived from the Cambridge Structural Database (CSD) have been used to perform a systematic conformational analysis for methylenecycloheptane, oxocycloheptane, azocycloheptane, oxepane, azepane and for the e-lactone and e-lactam fragments. Conformational mappings based on symmetry-adapted deformation coordinates and principal component scores show that ring conformations in these fragments fall almost exclusively on the chair-twist-chair pseudorotation pathway. Symmetry-modified Jarvis-Patrick clustering has been used to generate conformational classifications in a semi-automated manner. A manual classification was preferred for the oxocycloheptanes due to wide conformational diversity within a rather small data set. Energy calculations have also been carried out for these systems using force-field methods and a novel conformation-hunting algorithm that attempts to locate all local minima without recourse to ring cleavage and reformation. There is good qualitative agreement between the crystallographic observations of conformation and the calculated features of the potential energy hypersurface, despite the wide variety of substitution patterns covered by the crystallographic results.

Structural systematics. Part 4. Conformations of the diphosphine ligands in M2(µ-Ph2PCH2PPh2) and M(Ph2PCH2CH2PPh2) complexes

Data were retrieved from the Cambridge Structural Database for 405 crystal structures containing suitable geometric data for either M2(µ-dppm)1(dppm = Ph2PCH2PPh2) fragments (409 located) or M(dppe)2(M = transitional metal, dppe = Ph2PCH2CH2PPh2) fragments (274 such located). These data were analysed to examine the conformational preferences for the five-membered MP2C2(or M2P2C) rings and the attached phenyl groups. The technique of principal component analysis was used to reduce the dimensionality of the torsion angle data set and to aid in identification of favoured conformations. The M(dppe) fragments show a preference for a twist (C2) conformation of the MP2C2 five-membered ring, in which the P–C–C–P torsion angle is far from zero (typically ca. ±50°). In contrast the M2P2C five-membered rings of the M2(µ-dppm) fragments are predominantly of the envelope (Cs) conformation, with the methylene carbon out of the plane of the near-planar M2P2 unit, i.e. having the P–M–M–P torsion angle close to zero and the M–P–C–P torsion angles ca. ±45°. The distribution of structures indicates that in both cases the ring conformations interconvert by a pseudo-rotation pathway, similar to those observed for other five-membered ring systems, in which planar intermediates are avoided. In both 1 and 2 the two phenyl groups on each phosphorus adopt conformations typical of one- and two-ring flip mechanisms of rotation. For M2(µ-dppm) there is considerable constraint of phenyl group orientation due to clashes between phenyl groups in axial sites on the envelope M2P2C ring. In contrast, although weak preferences may be seen in the phenyl group conformations for the M(dppe) fragments, these arise primarily because of contacts between the phenyl groups and the ethylene hydrogens of the MP2C2 ring and not due to transannular Ph ⋯ Ph contacts. The implications of these observations for the design of new diphosphine ligands are discussed.

Potential nonrigidity of the NO3 radical

The equilibrium geometry and vertical excitation energies of the nitrate radical (NO3) have been determined at the coupled-cluster singles and doubles level. Unlike most previous theoretical methods used to study this problem, the present calculations circumvent the difficulties associated with symmetry-broken orbitals by using a reference function composed of orbitals obtained in a closed-shell self-consistent field (SCF) calculation for the NO3 anion. Although these orbitals do not satisfy the SCF equations for NO3 itself, they turn out to be more suitable for the correlation problem in the neutral molecule than the unrestricted Hartree–Fock solution for NO3. Nevertheless, our calculations agree with most previous studies in predicting that the high-symmetry D3h structure of NO3 is not a minimum on the potential energy surface. The potential near the D3h point is relatively flat and has seven stationary points: three (equivalent) C2v minima with one long and two short N–O bonds; three (equivalent) C2v transition states with two long and one short N–O bonds; and the D3h structure, which is unstable with respect to the in-plane degenerate mode (e′) and is consequently a saddle point of index two. Exchange of the oxygen positions via pseudorotation around the D3h stationary point is predicted to be an extremely facile process with a barrier height of ≊190 cm−1, suggesting that the molecule may be spectroscopically nonrigid, belonging to a molecule symmetry group which is isomorphic with D3h, as observed experimentally. Excitation energies are calculated for both the D3h structure and points on the pseudorotation pathway, in order to predict differences between values obtained from photodetachment spectroscopy of the NO3 anion and those determined by direct excitation of NO3.