Automatic estimation of heats of atomization and heats of reaction

Various additivity schemes for estimating heats of atomization have been evaluated to test their usefulness for designing a computer program. The approach is based on the Allen scheme and uses parameters obtained from thermochemical data. In addition, a method has been developed which allows the direct calculation of reaction enthalpies. Only the immediate environment of the bonds involved in the reaction has to be scanned. A program based on this method utilizes thermochemical parameters, too. Computation times with this program are extremely short and independent of the size of the molecules participating in the reaction. The procedure can be applied to a large variety of organic compounds. Examples demonstrate the accuracy of the predicted values.     

Molecular mechanics calculations on carbonyl compounds. IV. Heats of formation

Molecular mechanics (MM4) calculations on the heats of formation of aldehydes and ketones were carried out for a total of 59 compounds (10 aldehydes and 49 ketones). Optimization of the heat of formation parameters was obtained by a least squares fit to the experimentally known heats of formation. With the optimized MM4 heat of formation parameters, the MM4 calculated heats of formation showed significant improvement over those of MM3. The standard and weighted root mean square deviations for the MM4 values were 0.35 and 0.31 kcal mol^?1, respectively, whereas for the MM3 values they were 0.42 and 0.39 kcal mol^?1, respectively. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1476–1483, 2001     

链烷的物理化学性质及其分子参数的相关性研究

用N，N'，P，q,n等分子参数表征链烷的分子大小、取代参量和相邻取代基的 相互作用，并以其为独立参量，通过回归方法建立模型来预测链烷的某些物理化学 性质，对1-9个碳原子链烷的原子化焓、标准生成焓、汽化焓等理化性质的预测表 明该模型的原理简单、方法实用、结果可靠。其预测值民实验值吻合良好，且置信 度高达99.5%。     

Thermochemical parameters for benzenoid hydrocarbons

The heats of atomization of aromatic hydrocarbons are correlated with an incremental 5-term scheme that includes CH and CC bond energy terms, resonance energies, and two steric parameters. Regression analysis of the experimental data with respect to the proposed parameters gives reasonable values for each term. A simple method for calculating resonance energies is illustrated that agrees with the results of SCFLCAOMO calculations.     

Approaches to charge calculations in molecular mechanics

Alternative methods of estimating atomic charges in haloalkanes are presented, derived from quantum mechanical and classical treatments. A scheme based on a breakdown of the transmission of charge by polar atoms into one-bond, two-bond, and three-bond additive contributions is given, in which the one-bond effect is proportional to the difference in the electronegativities of the bonded atoms, and the two- and three-bond effects functions of the atomic electronegativity and polarizability. Suitable developments of the basic scheme, including an iterative self-consistent process, give calculated dipole moments for a variety of haloalkanes in good agreement with the observed values. The atomic charges obtained by this scheme are compared with other estimates of these charges. They are similar to those derived from a simple LCAO –MO scheme but differ from those obtained by population analysis of more refined quantum mechanical calculations.     

Approaches to charge calculations in molecular mechanics. 2 Resonance effects in conjugated systems

A previously published scheme of estimating atomic charges in haloalkanes is extended to include olefines, alcohols amines, acids, ethers, and amides. In the conjugated systems the effects of mesomeric transfer of charge are explicitly included. Generally good agreement with the observed dipole moments of these compounds and their substituted derivatives is found. The atomic charges so obtained are compared with those of other semiempirical and quantum-mechanical calculations for the amide group. The charges so obtained fall within the range of values obtained by these other schemes, supporting the general validity of this approach.     

Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules

The net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom-centered point-charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley & Sons, Inc.     

Molecular mechanics and molecular shape: Part VI. The response of simple molecules to bimolecular association

A molecular-mechanical force field, originally developed to calculate the structure and conformation of single molecules, has been applied to pairs of identical molecules lying at close proximity. The prototypes examined are very simple - short alkanes and short haloalkanes - but do include cases with conformational diversity and possible electrostatic effects. The optimized mutual orientations include the parallel alignment of linear alkanes, head-to-tail orientations of haloalkanes, as well as the head-to-head association, known from the crystallographic literature. The effect of aggregation on the conformation of the separate partners has been studied, and the intramolecular response characterized: in all cases examined, the partners contract. The computed energy gains are of the expected order of magnitude, the main contribution coming always from what molecular-mechanists label “non-bonded attraction”. Graphical representations of optimized orientations show the “protrusion-in-cleft” matching of molecular surfaces.     

Heats of formation of boron hydride anions and dianions and their ammonium salts [BnHmy-][NH4+]y with y=1-2

Thermochemical parameters of the closo boron hydride BnHn2- dianions, with n=5-12, the B3H8- and B11H14- anions, and the B5H9 and B10H14 neutral species were predicted by high-level ab initio electronic structure calculations. Total atomization energies obtained from coupled-cluster CCSD(T)/complete basis set (CBS) extrapolated energies, plus additional corrections were used to predict the heats of formation of the simplest BnHmy- species in the gas phase in kcal/mol at 298 K: DeltaHf(B3H8-)=-23.1+/-1.0; DeltaHf(B5H52-)=119.4+/-1.5; DeltaHf(B6H62-)=64.1+/-1.5; and DeltaHf(B5H9)=24.1+/-1.5. The heats of formation of the larger species were evaluated by the G3 method from hydrogenation reactions (values at 298 K, in kcal/mol with estimated error bars of+/-3 kcal/mol): DeltaHf(B7H72-)=51.8; DeltaHf(B8H82-)=46.1; DeltaHf(B9H92-)=24.4; DeltaHf(B10H102-)=-12.5; DeltaHf(B11H112-)=-11.8; DeltaHf(B12H122-)=-86.3; DeltaHf(B11H14-)=-57.3; and DeltaHf(B10H14)=18.7. A linear correlation between atomization energies of the dianions and energies of the BH units was found. The heats of formation of the ammonium salts of the anions and dianions were predicted using lattice energies (UL) calculated from an empirical expression based on ionic volumes. The UL values (0 K) of the BnHn2- dianions range from 319 to 372 kcal/mol. The values of UL for the B3H8- and B11H14- anions are 113 and 135 kcal/mol, respectively. The calculated lattice energies and gas-phase heats of formation of the constituent ions were used to predict the heats of formation of the ammonium crystal salts [BnHmy-][NH4+]y. These results were used to evaluate the thermodynamics of the H2 release reactions from the ammonium hydro-borate salts.     

Additivity methods for prediction of thermochemical properties. The Laidler method revisited. 2. Hydrocarbons including substituted cyclic compounds

A revised parameterization of the extended Laidler method for predicting standard molar enthalpies of atomization and standard molar enthalpies of formation at T = 298.15 K for several families of hydrocarbons (alkanes, alkenes, alkynes, polyenes, poly-ynes, cycloalkanes, substituted cycloalkanes, cycloalkenes, substituted cycloalkenes, benzene derivatives, and bi and polyphenyls) is presented. Data for a total of 265 gas-phase and 242 liquid-phase compounds were used for the calculation of the parameters. Comparison of the experimental values with those obtained using the additive scheme led to an average absolute difference of 0.73 kJ · mol⁻¹ for the gas-phase standard molar enthalpy of formation and 0.79 kJ · mol⁻¹ for the liquid-phase standard molar enthalpy of formation. The database used to establish the parameters was carefully reviewed by using, whenever possible, the original publications. A worksheet to simplify the calculation of standard molar enthalpies of formation and standard molar enthalpies of atomization at T = 298.15 K based on the extended Laidler parameters defined in this paper is provided as supplementary material.     

Gas‐phase and liquid‐state properties of esters,nitriles, and nitro compounds with the OPLS‐AA force field

Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1340–1352, 2001     

Calorimetric studies of the heats of formation of IIIB-VB adamantine phases

The techniques of precipitation calorimetry and solution calorimetry, with molten tin as the solvent medium, have been used to measure the heats of formation of six IIIB-VB semiconductor compounds. Standard heats of formation of 298 K obtained from these measurements are: AIP (?17.41), AIAs (?14.43), AISb (?5.97), GaP (?12.49), GaAs (?9.76) and InP (?6.75) ?k cal g atom^?1. These and other data are used to examine the validity of published theoretical estimates of the heats of formation of these phases. The interrelation of their heats of atomization and energy band gaps is briefly discussed.     

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.     

Heats of formation of beryllium, boron, aluminum, and silicon re-examined by means of W4 theory

Benchmark total atomization energies (TAE0 values) were obtained, by means of our recent W4 theory [Karton, A.; Rabinowitz, E.; Martin, J. M. L.; Ruscic, B. J. Chem. Phys. 2006, 125, 144108], for the molecules Be2, BeF2, BeCl2, BH, BF, BH3, BHF2, B2H6, BF3, AlF, AlF3, AlCl3, SiH4, Si2H6, and SiF4. We were then able to deduce "semi-experimental" heats of formation for the elements beryllium, boron, aluminum, and silicon by combining the calculated TAE0 values with experimental heats of formation obtained from reactions that do not involve the species Be(g), B(g), Al(g), and Si(g). The elemental heats of formation are fundamental thermochemical quantities that are required whenever a molecular heat of formation has to be derived from a calculated binding energy. Our recommended DeltaH degrees f,0 [A(g)] values are Be 76.4+/-0.6 kcal/mol, B 135.1+/-0.2 kcal/mol, Al 80.2+/-0.4 kcal/mol, and Si 107.2+/-0.2 kcal/mol. (The corresponding values at 298.15 K are 77.4, 136.3, 80.8, and 108.2 kcal/mol, respectively.) The Be value is identical to the CODATA recommendation (but with half of the uncertainty), while the B, Al, and Si values represent substantial revisions from established earlier reference data. The revised B and Si values are in agreement with earlier semi-ab initio derivations but carry much smaller uncertainties.     

Electrostatic model for infrared intensities in a spectroscopically determined molecular mechanics force field

A new electrostatic model for the calculation of infrared intensities in molecular mechanics and molecular dynamics is presented. The model is based on atomic charges, atomic charge fluxes, and internal coordinate dipoles and their fluxes. The internal coordinate dipoles are used instead of atomic dipoles, thus simplifying the derivation of parameters. The model is designed to reproduce ab initio dipole derivatives, and the parameters can be obtained by (iterative) transformations from these, or by linear least squares fitting to them. A first application to linear alkanes has been made. For these molecules, the intensities can be predicted with an average accuracy of 30–40%. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 754–768, 1998     

Linear calibrations in chromatography: The incorrect use of ordinary least squares for determinations at low levels,and the need to redefine the limit of quantification with this regression model

Ordinary least squares is widely applied as the standard regression method for analytical calibrations, and it is usually accepted that this regression method can be used for quantification starting at the limit of quantification. However, it requires calibration being homoscedastic and this is not common. Different calibrations have been evaluated to assess whether ordinary least squares is adequate to quantify estimates at low levels. All calibrations evaluated were linear and heteroscedastic. Despite acceptable values for precision at limit of quantification levels were obtained, ordinary least squares fitting resulted in significant and unacceptable bias at low levels. When weighted least squares regression was applied, bias at low levels was solved and accurate estimates were obtained. With heteroscedastic calibrations, limit values determined by conventional methods are only appropriate if weighted least squares are used. A “practical limit of quantification” can be determined with ordinary least squares in heteroscedastic calibrations, which should be fixed at a minimum of 20 times the value calculated with conventional methods. Biases obtained above this “practical limit” were acceptable applying ordinary least squares and no significant differences were obtained between the estimates measured using weighted and ordinary least squares when analyzing real‐world samples.     

An improved empirical force field for saturated hydrocarbons

A new molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well-known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.     

烯烃在USY沸石表面上化学反应热的量热测定

1.前言 在多相催化研究工作中,测定反应物分子在固体催化剂表面上化学吸附时产生的反应热,或者说化学吸附热,对研究催化剂的性质和反应物的表面化学反应都很有帮助。但是目前尚无有效的方法测定它。本文用吸附量热法测定了烯烃在USY沸石表面的吸附热,并提出了一种化学吸附热的估算方法。