The effects of fluorine and chlorine substitution on bond lengths in ethanes and disilanes: comparisons of ab initio and experimental information

Ab initio and some density functional theory calculations of bond lengths in fluoro- and chloro-ethanes and disilanes are reported with a precision of ±0.0001 Å under strictly comparable conditions. The resulting changes in MH and MX (M=C, Si; X=F, Cl) bond length are analysed for the effects of halogens substituted in geminal (), or vicinal (gauche or trans) positions. The shortening effect of halogen on an MH bond is markedly reduced or even reversed by the introduction of electron correlation at the MP2 or B3LYP level. MX bonds are little affected. gauche halogen consistently shortens both MH and MX bonds, while trans halogen has no effect on an MH bond but a small and variable effect on the MX bond.

The reality of these calculated changes in bond length is tested in two ways. MH bond lengths are plotted against experimental values of the isolated stretching frequencies ν^isMH, which themselves correlate well with experimental r₀ bond lengths. Agreement on the resulting substituent effects is generally good for the gauche and trans effects of halogen but variable for effects. Unobserved ν^isMH values are predicted from computed bond lengths in fluoroethanes, chloroethanes and chlorodisilanes.

Calculated MX and MM bond lengths are compared with experimental values, notably those from electron diffraction studies amongst the ethanes. Most calculations underestimate the changes found experimentally in CF and CCl bond lengths. CC bond length changes are underestimated in fluoroethanes and overestimated in the chloro-compounds.

The ‘offset’ value (r_e(calc)−r_e(true)) for a CH or SiH bond calculated with a given basis set and level of theory in most cases varies markedly throughout the series of compounds. The same is true for CF, CCl, CC and SiSi bonds if the corresponding offset values for the r_a lengths are constant.

The need is stressed for extended experimental work on many of the compounds, especially the disilanes. It is recommended that structures should be refined with ab initio derived constraints on the bond lengths involved and differences between spectroscopic and diffraction-based geometries reconciled through the calculation of r_z structures.     

The variation of carbon-carbon bond lengths with environment as determined by spectroscopic studies of simple polyatomic molecules

A brief and critical review of the spectroscopic method of determining molecular structures is given. The difficulties and present experimental accuracies of the method are discussed and comparisons with available diffraction values are made. Spectroscopic data on carbon-carbon bond lengths (accurate to 0·005 Å) which have been accumulated in recent years are summarized. These show a simple dependence on bond environment, namely, that bond lengths increase linearly with an increase in the number of adjacent bonds.     

Dynamic bond constraints in protein Langevin dynamics

Bond constraint algorithms for molecular dynamics typically take, as the target constraint lengths, the values of the equilibrium bond lengths defined in the potential. In Langevin form, the equations of motion are temperature dependent, which gives the average value for the individual bond lengths a temperature dependence. In addition to this, locally constant force fields can shift the local equilibrium bond lengths. To restore the average bond lengths in constrained integration to their unconstrained values, we suggest changing the constraint length used by popular constraint methods such as RATTLE [H. C. Andersen, J. Comput. Phys. 52, 23 (1983)] at each step. This allows us to more accurately capture the equilibrium bond length changes (with respect to the potential) due to the local equilibration and temperature effects. In addition, the approximations to the unconstrained nonbonded energies are closer using the dynamic constraint method than a traditional fixed constraint algorithm. The mechanism for finding the new constrained lengths involves one extra calculation of the bonded components of the force, and therefore adds O(N) time to the constraint algorithm. Since most molecular dynamics calculations are dominated by the O(N2) nonbonded forces, this new method does not take significantly more time than a fixed constraint algorithm.     

Silicon nanotubes with distinct bond lengths

In this paper, we extend both the rolled-up and the polyhedral models for single-walled silicon nanotubes with equal bond lengths to models having distinct bond lengths. The silicon nanotubes considered here are assumed to be formed by sp³ hybridization with different bond lengths so that the nanotube lattice is assumed to comprise only skew rhombi. Beginning with the three postulates that all bonds lying on the same helix are equal, all adjacent bond angles are equal, and all atoms are equidistant from a common axis of symmetry, we derive exact formulae for the polyhedral geometric parameters such as chiral angles, bond angles, radius and unit cell length. The polyhedral model presented here with distinct bond lengths includes both the rolled-up model with distinct bond lengths which arises from the first term of an asymptotic expansion, and an existing polyhedral model of the authors which assumes equal bond lengths. Finally, some molecular dynamics simulations are undertaken for comparison with the geometric model. These simulations start with equal bond lengths and then stabilize in such a way that two distinct bond lengths emerge.     

Two-dimensional Hückel molecular orbital theory

The simple Hückel molecular orbital theory is extended to include hydrocarbons with sp-hybridization in addition to the sp²-hybridization. Molecular orbitals are constructed as linear. combinations of 2p orbitals in two dimensions perpendicular to each other. Total π bond orders (P) are defined and cover the range up to P = 2 in the two-dimensional case. The relationship between bond orders and CC bond lengths is studied. The theory is applied to nine hydrocarbons, which include systems with conjugated and cumulated double bonds as well as triple bonds. Calculated bond lengths from the bond orders are found to agree within ±0.03 Å with experimental values.     

Normalkonformationen achtgliedriger Heterocyclen mit transannular gebundenem Germanium,Zinn, Arsen und Antimon

Standard Conformations of 8-Membered Heterocycles with Transannular Bonded Germanium, Tin, Arsenic, and Antimony Standard values of conformations, bond lengths, coordinations of the element, and bond angles are given and discussed for 1,3,6-trichalcogena-2-elementocanes with chlorine substituted element Ge, Sn, As, and Sb, respectively.     

Bond lengths in cyclic polyenes C2nH2n a re-examination from the valence-bond point of view

The valence-bond resonance method for predicting bond lengths in conjugated hydrocarbon molecules has been reconsidered. New values are obtained for the variation of the fundamental exchange and Coulomb integrals with bond length. Application to the cyclic polyenes C_2nH_2n shows that for large n there will be substantial bond alternation. Inclusion of Dewar structures diminishes this alternation, but does not destroy it.     

4‐Amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one (metamitron) and 4‐amino‐6‐methyl‐3‐phenyl‐1,2,4‐triazin‐5(4H)‐one (isometamitron)

The title structures, both C₁₀H₁₀N₄O, are substitutional isomers. The N—N bond lengths are longer and the C=N bond lengths are shorter by ca 0.025 Å than the respective average values in the C=N—N=C group of asymmetric triazines; the assessed respective bond orders are 1.3 and 1.7. There are N—H⋯O and N—H⋯N hydrogen bonds in both structures, with 4‐­amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one containing a rare bifurcated N—H⋯N,N hydrogen bond. The structures differ in their mol­ecular stacking and the hydrogen‐bonding patterns.     

Benchmarking of model core potentials: application to the halogen complexes of group 4 metals

The reliability of the model core potential (MCP) method was probed in a systematic RHF and MP2 study of the geometries of the group 4 metal halogen complexes (MX4; M = Ti, Zr, Hf and X = F, Cl, Br, I). The computed bond lengths were compared with experimental values, as well as those predicted using effective core potentials. Provided that electrons from the outermost core shell of the metal atom are treated explicitly in the calculation, both the MCP and ECP methods predict M-X bond lengths within 0.02-0.03 A of experiment. The reaction energies for a simple set of halogen substitution reactions of the MX4 complexes leading to the mixed halogen complex, MX2Y2, were also studied. Although no experimental values are available for these reactions, comparison was made with the values computed using effective core potentials. The predictability of the different pseudopotential techniques and the importance of the metal atom valence basis set contraction scheme and polarization space are discussed.     

Vibrational spectroscopic study of hydrated uranyl oxide: Curite

Raman and infrared spectra of the uranyl oxyhydroxide hydrate: curite is reported. Observed bands are attributed to the (UO₂)²⁺ stretching and bending vibrations, U–OH bending vibrations, H₂O and (OH)⁻ stretching, bending and librational modes. U–O bond lengths in uranyls and O–H…O bond lengths are calculated from the wavenumbers assigned to the stretching vibrations. These bond lengths are close to the values inferred and/or predicted from the X-ray single crystal structure. The complex hydrogen-bonding network arrangement was proved in the structures of the curite minerals. This hydrogen bonding contributes to the stability of these uranyl minerals.     

17O NMR studies of substituted 1,3,4-oxadiazoles

Three series of substituted 1,3,4-oxadiazoles were studied by (17)O NMR spectroscopy. Chemical shifts values were correlated with empirical Hammett parameters as well as calculated bond lengths and chemical shielding values.     

Das Pyren und der Einfluß von Substitution oder Komplexie-rung auf seine Geometrie und Packung im kristallinen Zustand

The crystal structures of pyrene and substituted and complexed derivatives of pyrene have been investigated by X-ray and neutron diffraction. The geometry of the pyrene skeleton has been determined experimentally with high accuracy and calculated by quantum chemical methods. In the cases reported in the literature and cited here the pyrene skeleton has the molecular symmetry mmm or mm2 with values for the bond lengths of the six symmetrically independent bondsa, b, c, d, e, f differing significantly in the limits of error. Mean values of a number of experimental and theoretical bond lengths are given and can be considered as standard values for the mm2 symmetric pyrene skeleton. In the case of substitution of the pyrene in 3-position with a polar heterocyclic molecule of the azomethine-imine type the mm2 symmetry vanishes, a C–H ... N intramolecular hydrogen bond arises and the directly neighbouring pyrene units are not packed parallel with their planes to each other, but they are considerably tilted. Relatively narrow intermolekular C-C contacts, 3.314 and 3.368 Å, have been observed. The conclusion is drawn that the asymmetry of the pyrene molecule and a tilt of directly neighbouring pyrene units in the crystal packing can be induced by substitution e. g. with suitable polar heterocycles.

Juli 1985.     

MNDO Calculations of silicon-containing molecules

A comparison is made of MNDO and MINDO /3 calculations for saturated silicon-containing molecules, and with experimental values, for heats of formation, molecular geometries, charge distributions, and ionization potentials. Except for bond angles, it is found that with the published parameter values the MINDO /3 program gives more reliable results than MNDO . For unsaturated molecules, a comparison of bond lengths and stabilities of Si multiple bonds as given by the two programs and ab initio methods is made, and large discrepancies between predicted structures are pointed out. Some reasons for the dicrepancies are discussed.     

六氟乙烷分解成氟甲基及其逆反应的A因子和活化能的计算

采用半经典统计方法对过渡态的临界键长进行了具体计算,利用这些结果计算了CF_3+CF_3C_2F_6反应的指数前因子和活化能,计算结果与实验值相当符合。     

Structural correlations in liquid water: a new interpretation of IR spectroscopy

We present a new and alternative interpretation of the structure of the IR vibrational mode (nu(OH) band) of pure water. The re-interpretation is based on the influence of the cooperative hydrogen bonding arising from a network of hydrogen bonds in the liquid. The nu(OH) band has six components that are dominated by differences in their O-H bond lengths but deviate from thermodynamically average values due to interactions with the hydrogen bond network. The physical origin of the structure in the nu(OH) band is directly related to the O-H bond length, and variations in this bond length are caused by the influence of the surrounding hydrogen-bonded network of water molecules.     

Effects of chain length on the rates of C-C bond dissociation in linear alkanes and polyethylene

Molecular dynamics modeling of C-C bond dissociation is performed for a series of linear alkanes and polyethylene macromolecules with the chain lengths ranging from one to a thousand constituent ethylene monomers (PE-1-PE-1000). The rate constants obtained in molecular dynamics calculations are compared with those determined using variational transition state theory with the same potential energy surface. The results of simulations demonstrate a significant accelerating effect of chain length on the rates of C-C bond scission. Per-bond rate constant values increase with the increasing chain length, up to an order of magnitude, in the sequence of linear alkanes from PE-1 (ethane) to PE-5 (decane); this dependence becomes saturated for longer chain lengths. Stiffening the potentials of bending and especially the torsional degrees of freedom diminishes the accelerating effect of chain length, while constraining the bond distances for all C-C bonds except the one undergoing dissociation has no effect. The results of the calculations are compared with existing experimental data on the dependences of the rates of thermal decomposition of linear alkanes on the alkane chain length.     

Linear carbon chains of type SiCnO (n = 3-8): results of coupled cluster calculations

On the basis of (R)CCSD(T) calculations with the cc-pVQZ basis set, accurate equilibrium bond lengths (ca. 0.0005 A accuracy) are established for linear carbon chains of type SiCnO with n = 3-8. SiC and CO equilibrium bond lengths are in the range 1.683-1.735 and 1.165-1.167 A, respectively. A narrow range (1.272-1.287 A) is obtained for all 25 carbon-carbon equilibrium distances. The equilibrium dipole moments (mu(e)) exhibit large correlation effects. The mu(e) values for the closed-shell species with even integer n are larger than those for the triplet ground states of SiCnO chains with odd n values. Various spectroscopic constants such as harmonic vibrational wavenumbers, vibration-rotation coupling, and l-type doubling constants are calculated. The ground-state rotational constants of SiC3O, SiC4O, and SiC5O are predicted with ca. 0.1% accuracy to be 1386.5, 867.0, and 564.4 MHz.     

Polycyclic aromatic hydrocarbons with five-membered rings: Modeling of experimental X-ray and neutron-diffraction structures

Several of the readily available theoretical programs are evaluated as tools for modeling the structures of polycyclic aromatic hydrocarbons with five-membered rings (CPAHs). The experimentally determined bond lengths and angles are compared to calculated values. Experimental bond lengths are also compared to Pauling and Huckel molecular orbital (HMO) bond orders. Previously published experimental X-ray and neutron-diffraction structures of acenaphthene, acenaphthylene, fluoranthene, cyclopent[o,p,q,r]benz[c]phenanthrene, and corannulene are modeled by the programs MMX, AM1, MNDO, and PM3, and previously reported STO-3G and 6-31G * data are also evaluated. In general, the error differences between the experimental and calculated results for all of the semiempirical programs were small. However, PM3 performed slightly better than AM1 and MMX, while MNDO generated structures which exhibited the largest deviation from experiment. Although the standard deviations for all programs are shown to be of comparable magnitude, a particular bond length or bond angle in any given theoretical calculation can exhibit significant error from the experimental data. The scatter in the bond order data computed from Huckel molecular orbital theory and valence bond theory is contrary to results obtained with alternant systems. It appears that these approaches are less successful at modeling accurately the nonalternant hydrocarbon systems described in this paper.     

Extended Hückel theory: A new population analysis and its application to forecast chemical bond lengths

Although widely used, the population analysis proposed by Mulliken has been contested by several authors. A new analysis, very easily computed on the orthogonal basis, is here proposed and applied to the EHT wave function.Under its usual presentation, the EHT method is unable to directly evaluate bond lengths through an energy minimum condition. However, it is possible to settle an empirical quadratic relation between the bond lengthR _rs and a quantity calledp _rs, similar to a bond population. Such relations are given for bonds of the CC, CN, CO, CS, CF, CCl, CBr, CH, NO and OH types.The examination of the variation of the bond population under a variation of the bond length has enabled us to prove that this semi-empirical relation was usable in an iterative process: starting from bond lengths taken from any systematic table, it is possible, for a given molecule, to evaluate the bond length consistent with experimental values within an accuracy of 0.03 Å. Some examples, concerning cyclic or acyclic molecules and various kinds of bonds, are given.     

Molecular parameters for the prediction of polyurethane structures

Recent efforts to determine the structures of poly(MDI/diol) hard segments in polyurethane elastomers have relied on the structures determined by single-crystal x-ray methods for diphenylmethane urethane model compounds. We have surveyed the structure of six model compounds, and have derived average values for the bond lengths, bond angles, and bond torsion angles for use in future analyses. The applicability of these averages to polymer structures is discussed, and the data are used to derive models for the poly(MDI-butanediol) chain which are found to be consistent with the fiber repeat determine by x-ray methods.