Structure and bonding in square-planar chalcogen rings

1992 ◽  
Vol 70 (2) ◽  
pp. 348-352 ◽  
Author(s):  
Leif J. Saethre ◽  
Odd Gropen
Keyword(s):  
Potential Model ◽  
Population Analysis ◽  
Atomic Charge ◽  
Molecular Structures ◽  
Basis Set ◽  
Single Bond ◽  
Bond Lengths ◽  
Square Planar ◽  
Structure And Bonding ◽  
D Orbitals

The molecular structures of square-planar X42+, X4+, and X4 (X = S, Se, Te) have been calculated using the effective core potential model. For X42+ the agreement between experimental and calculated values is excellent provided that d orbitals are included in the basis set. For the hypothetical molecules X4+ and X4 the bond lengths are found to increase dramatically as one and, subsequently, two electrons are added to the systems. Extensive population analysis shows that this increase is almost exclusively due to loss of bonding in the π system, whereas the bonding in the σ system remains relatively unaltered. These results make it possible to predict covalent single bond radii for S, Se, and Te for which the influence of π repulsion is removed. From the calculated variation of bond lengths with atomic charge, bond lengths are predicted for a series of planar disulphide rings. Keywords: structure, bonding, chalcogen, theoretical, ECP.

scholarly journals Comparison of molecular structures of cis-bis[8-(dimethylphosphanyl)quinoline]nickel(II) and -platinum(II) complex cations

2020 ◽  
Vol 76 (12) ◽  
pp. 1813-1817
Author(s):  
Masatoshi Mori ◽  
Takayoshi Suzuki
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Molecular Structures ◽  
Coordination Geometry ◽  
Donor Group ◽  
Bending Deformation ◽  
Bond Lengths ◽  
Square Planar ◽  
Chelate Ligands

The crystal structures of the complexes (SP-4-2)-cis-bis[8-(dimethylphosphanyl)quinoline-κ2 N,P]nickel(II) bis(perchlorate) nitromethane monosolvate, [Ni(C11H12NP)2](ClO4)2·CH3NO2 (1), and (SP-4-2)-cis-bis[8-(dimethylphosphanyl)quinoline-κ2 N,P]platinum(II) bis(tetrafluoroborate) acetonitrile monosolvate, [Pt(C11H12NP)2](BF4)2·C2H3N (2), are reported. In both complex cations, two phosphanylquinolines act as bidentate P,N-donating chelate ligands and form the mutually cis configuration in the square-planar coordination geometry. The strong trans influence of the dimethylphosphanyl donor group is confirmed by the Ni—N bond lengths in 1, 1.970 (2) and 1.982 (2) Å and, the Pt—N bond lengths of 2, 2.123 (4) and 2.132 (4) Å, which are relatively long as compared to those in the analogous 8-(diphenylphosphanyl)quinoline complexes. Mutually cis-positioned quinoline donor groups would give a severe steric hindrance between their ortho-H atoms. In order to reduce such a steric congestion, the NiII complex in 1 shows a tetrahedral distortion of the coordination geometry, as parameterized by τ4 = 0.199 (1)°, while the PtII complex in 2 exhibits a typical square-planar coordination geometry [τ4 = 0.014 (1)°] with a large bending deformation of the ideally planar Me2Pqn chelate planes. In the crystal structure of 2, three F atoms of one of the BF4 − anions are disordered over two sets of positions with refined occupancies of 0.573 (10) and 0.427 (10).

Purine complexes of platinum: synthesis, nmr, and crystal and molecular structures of cis-chloro(caffeine)bis(triethylphosphine)platinum(II) fluoroborate and cis-bis(isocaffeine)bis(triethylphosphine)platinum (II) fluoroborate

1983 ◽  
Vol 61 (6) ◽  
pp. 1132-1141 ◽  
Author(s):  
Gordon William Bushnell ◽  
Roderick James Densmore ◽  
Keith Roger Dixon ◽  
Arthur Charles Ralfs
Keyword(s):  
Crystal Structure ◽  
Nmr Spectra ◽  
Molecular Structures ◽  
Platinum Drugs ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Bond Lengths ◽  
Antitumour Agents ◽  
Crystal And Molecular Structures ◽  
Square Planar

Synthesis and 31P nmr spectra of the complex cations, cis-[PtCl(L)(PEt3)2]+, L= theophylline, caffeine, or isocaffeine, and cis[Pt(isocaff)2(PEt3)2]2+ are reported. The crystal structure of cis-[PtCl(caffeine)(PEt3)2][BF4] is determined, space group [Formula: see text], a = 1.1766(6), b = 1.4428(5), c = 0.9002(4) nm, α = 97.28(4)°, β = 97.69(4)°, γ = 100.96(5)°, Dm = 1.649 g cm−1, the bond lengths are Pt—Cl= 233.4(4) pm, Pt—N = 215(1) pm, Pt—P = 225.4(5) pm (mean), and the residual R = 0.071. The crystal structure of cis-[Pt(isocaffeine)2(PEt3)2][BF4]2 is orthorhombic, space group Pbca, a = 2.317(3), b = 1.717(3), c = 2.130(3) nm, Dm = 1.574 g cm−3, with an opposing isocaffeine conformation, bond lengths Pt—N = 211(2) pm, Pt—P = 227.6(9) pm (mean), and R = 0.073. Both crystal structures contain approximately square planar Pt(II) coordination with the purine coordinated via an imidazole nitrogen. The structures are discussed as models for the possible involvement of [Formula: see text] chelation of guanine to platinum when platinum drugs act as antitumour agents, but there is no evidence that isocaffeine acts as an [Formula: see text] chelate.

Nonadditive effects of polysubstitution in CH4 and CH3: a test of abinitio and semiempirical MO methods

1983 ◽  
Vol 61 (7) ◽  
pp. 1567-1572 ◽  
Author(s):  
N. Colin Baird
Keyword(s):  
Basis Set ◽  
Semiempirical Methods ◽  
Valence Shell ◽  
Bond Lengths ◽  
Hartree Fock ◽  
Nonadditive Effects ◽  
D Orbitals ◽  
Split Valence ◽  
Abinitio Calculations

The effects to the bond lengths and molecular energy of making multiple substitutions at the same carbon atom in methane and the methyl free radical are studied using various molecular orbital methods. All abinitio calculations were based upon the Hartree–Fock formalism (unrestricted in the case of free radicals) and employed the STO-3G (with d orbitals on chlorine), 3-21G, and 4-31G bases, the last both with and without a set of Gaussian d orbitals on the carbon. The semiempirical methods used were the MINDO/3 and MNDO methods of Dewar and co-workers; computations for polysubstituted ethanes by these two methods also arc reported. The abinito methods which use a split valence shell basis set account very well for the trends in bond lengths and heats of formation, at least when the polysubstituent is fluorine or hydroxyl. In contrast, the semiempirical calculations and the abinitio STO-3G results gave very poor results. Finally, the role of interactions between the AH bonds in a variety of hydrides AHn is illustrated using experimental energetics.

Basis set dependence, precision, and accuracy of fullab initiogradient optimizations of molecular structures of nonstrained hydrocarbons. I. CC bond lengths

1989 ◽  
Vol 10 (3) ◽  
pp. 329-343 ◽  
Author(s):  
Günter Häfelinger ◽  
Claus Ulrich Regelmann ◽  
Tadeusz Marek Krygowski ◽  
Krzysztof Wozniak
Keyword(s):  
Molecular Structures ◽  
Basis Set ◽  
Bond Lengths ◽  
Precision And Accuracy

Conformational studies on cyclohexa-1,4-diene derivatives. The crystal and molecular structures of 1,2,4,5-tetraphenyl-3,6-dicarbomethoxycyclohexa-1,4-diene and 1,2-dicarbomethoxy-4,5-dimethylcyclohexa-1,4-diene

1978 ◽  
Vol 56 (10) ◽  
pp. 1358-1363 ◽  
Author(s):  
M. J. Bennett ◽  
J. T. Purdham
Keyword(s):  
Direct Methods ◽  
Molecular Structures ◽  
Monoclinic Space Group ◽  
Single Bond ◽  
Orthorhombic Space Group ◽  
Small Deviations ◽  
Conformational Studies ◽  
Space Group ◽  
Bond Lengths ◽  
Least Squares Techniques

1,2,4,5-Tetraphenyl-3,6-dicarbomethoxycyclohexa-1,4-diene crystallizes in the monoclinic space group I2/a (a non-standard setting of C2/c) with a = 20.052(2), b = 5.756(1), c = 22.782(2) Å, β = 95.73(1)°, and Z = 4. 1,2-Dicarbomethoxy-4,5-dimethylcyclohexa-1,4-diene crystallizes in the orthorhombic space group Pbca with a = 25.627(2), b = 11.240(1), c = 8.342(1) Å, and Z = 8. Both structures were solved by direct methods and refined by full matrix least-squares techniques to R = 0.040 and R = 0.036, respectively. Carbon–carbon double bond lengths are similar in the two compounds (1.326 and 1.333 Å, respectively), but the single bond lengths are significantly longer in l,2,4,5-tetraphenyl-3,6-dicarbomethoxycyclohexa-1,4-diene (1.518 Å) compared with the 1.493 Å average found in 1,2-dicarbomethoxy-4,5-dimethyl- cyclohexa-1,4-diene. This and the fact that there are also small deviations from planarity in the former compound are thought to be due to the presence of substituents on the methylenic carbon atoms.

scholarly journals Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Raiker Witter ◽  
Margit Möllhoff ◽  
Frank-Thomas Koch ◽  
Ulrich Sternberg
Keyword(s):  
Force Field ◽  
Influenza A ◽  
Transmembrane Domain ◽  
Population Analysis ◽  
3D Structure ◽  
Atomic Charge ◽  
Basis Set ◽  
Atomic Charges ◽  
Molecular Mechanics Calculations ◽  
Activated State

Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges ofab initiocalculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation ofR=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angleχ1and small variations ofχ2of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

Abinitio molecular orbital calculations for SF4, SOF2, and SO2F2

1981 ◽  
Vol 59 (5) ◽  
pp. 814-816 ◽  
Author(s):  
N. Colin Baird ◽  
Kathleen F. Taylor
Keyword(s):  
Molecular Orbital ◽  
Sulfur Atom ◽  
Basis Set ◽  
Molecular Orbital Calculations ◽  
Constant Amount ◽  
Bond Lengths ◽  
Equilibrium Structures ◽  
Gaussian Orbitals ◽  
D Orbitals ◽  
Extended Basis

Abinitio molecular orbital calculations are reported for SF4 (both C2v and C4v symmetries), SOF2, and SO2F2. Geometry searches were conducted using the STO-3G* basis set; the energies were recalculated at the predicted equilibrium structures also using STO-3G and 44-31G, and the latter basis set with the addition of five real d Gaussian orbitals on the sulfur atom. The predicted geometries agree well with experiment, although S=O bonds are consistently predicted too long by ∼0.03 Å, and the variation in S—F bond lengths among different environments is underestimated. The energy stabilization associated with the addition of d orbitals is generally consistent with our previous calculations, i.e. it is a constant amount per bond in hypervalent sulfur compounds in extended basis calculations. Replacement of F by OH is predicted to be more exothermic in SO2F2 than in SOF2, and the relevance of this prediction to estimated heats of formation for SOF2 and SO(OH)2 is discussed.

The Solid State Conformation of Diaryl Ditellurides and Diselenides: The Crystal and Molecular Structures of (C4H3E2)2E'2 (E = O, S; E' = Te, Se)

2000 ◽  
Vol 55 (5) ◽  
pp. 361-368 ◽  
Author(s):  
Raija Oilunkaniemi ◽  
Risto S. Laitinen ◽  
Markku Ahlgrén
Keyword(s):  
Solid State ◽  
Lone Pair ◽  
Spectroscopic Properties ◽  
Molecular Structures ◽  
Dihedral Angles ◽  
Single Bond ◽  
Aromatic Rings ◽  
Bond Lengths ◽  
Crystal And Molecular Structures ◽  
Solid State Conformation

The crystal and molecular structures of dithienyl ditelluride (C4H3S)2Te2 (1), difuryl ditelluride (C4H3O)2Te2 (2), dithienyl diselenide (C4H3S)2Se2 (3), and difuryl diselenide (C4H3O)2Se2 (4) are reported in this paper and compared to those of other simple diaryl ditellurides and diselenides. The chalcogen-chajcogen bonds exhibit approximately single bond lengths [Te-Te = 2.7337(8) and 2.7240(4) Å in 1 and 2, respectively; Se-Se = 2.357(1) and 2.368(2) Å in 3 and 4, respectively], as do the chalcogen-carbon bond lengths [Te-C = 2.095(9) - 2.104(6) in 1 and 2.091(6) - 2.105(9) Å in 2; Se-C = 1.87(1) - 1.90(1) Å in 3 and 1.887(8) - 1.897(10) Å in 4]. The aromatic rings are disordered. The dihedral angles C-E-E-C range from 79(2) to 96(1)° are consistent with the concept of minimized p lone-pair repulsion of adjacent chalcogen atoms. The dependence of molecular parameters on the angle between the aromatic rings and the chalcogen-chalcogen bonds follow trends established previously for aromatic disulfides. Though the bond parameters and conformations of 1 - 4 are similar, the packing of the molecules is different. The two ditellurides 1 and 2 show short Te···Te contacts (3.900 - 4.002 Å in 1 and 4.060 - 4.172 Å in 2). The two diselenides 3 and 4 do not exhibit close chalcogen-chalcogen interactions. The NMR spectroscopic properties of 1 - 4 are discussed.

PROBING THE INTERPLAY BETWEEN MULTIPLICITY AND IONICITY OF THE CHEMICAL BOND

2011 ◽  
Vol 10 (04) ◽  
pp. 471-482 ◽  
Author(s):  
DARIUSZ SZCZEPANIK ◽  
JANUSZ MROZEK
Keyword(s):  
Chemical Bond ◽  
Population Analysis ◽  
Atomic Charge ◽  
Numerical Results ◽  
Basis Set ◽  
Chemical Bonds ◽  
Bond Multiplicity ◽  
Bond Covalency ◽  
Type Bond

A new bond multiplicity measure based on the Wiberg-type bond covalency index and the atomic charge from population analysis is presented. Heuristically derived formulas allow one to evaluate the character of the chemical bond, especially its ionicity degree. Numerical results at RHF/ROHF theory level demonstrate that full multiplicities of typical chemical bonds are close to formal orders and their basis set dependence is inconsiderable, especially for highly polarized chemical bonds.

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