Prediction Of Bond Dissociation Energies Research Articles

Determination of Bond Dissociation Energies Using Electrospray Tandem Mass Spectrometry and a Derived Effective Reaction Path Length Approach

A new approach for calculating bond dissociation energies (BDEs) from ES-MS/MS measurements has been developed. The new method features a "derived effective reaction path length" that has been applied to measure BDEs of alkali metal (Li+) adducts and halide (Cl-) adducts of monoacylglycerol, 1,2-diacylglycerol, and 1,3-diacylglycerol lipids. Also studied were lithium-bound dimers of monoacylglycerols, 1,2-diacylglycerols, and 1,3-diacylglycerols. BDEs for the adducts and dimers of the lipids were derived from collision-induced dissociation experiments using a triple quadrupole mass spectrometer with electrospray as the ionization source. Mass spectral data were used to empirically derive a single-exponential growth equation that relates product cross section to collision energy. From these single-exponential equations, a general second-order polynomial was derived using a multivariate growth curve model that enables prediction of BDEs of unknown complexes. Mass spectral results were compared to computer-generated bond dissociation energies using Becke-style three-parameter density functional theory (B3LYP, employing the Lee-Yang-Parr correlation functional), with excellent agreement between experimental and theoretical energy values. The newly developed method is general in nature and can be used for the measurement of metal or halide ionic adduct bond dissociation energies and for the measurement of bond energies of noncovalent interactions such as dimer dissociation energies. The validity of the method has been rigorously established using a triple quadrupole, but it may also be applied to other mass spectrometers that allow user control of the collision cell potential.

Size extensive modification of local multireference configuration interaction.

We recently developed a reduced scaling multireference configuration interaction (MRCI) method based on local correlation in the internal (occupied) and external (virtual) orbital spaces. This technique can be used, e.g., to predict bond dissociation energies in large molecules with reasonable accuracy. However, the inherent lack of size extensivity of truncated CI is a disadvantage that in principle worsens as the system size grows. Here we implement an a priori size-extensive modification of local MRCI known as the averaged coupled pair functional (ACPF) method. We demonstrate that local MR-ACPF recovers more correlation energy than local MRCI, in keeping with trends observed previously for nonlocal ACPF. We test the size extensivity of local ACPF on noninteracting He atoms and a series of hydrocarbons. Basis set and core correlation effects are explored, as well as bond breaking in a variety of organic molecules. The local MR-ACPF method proves to be a useful tool for investigating large molecules and represents a further improvement in predictive accuracy over local MRCI.

Bond dissociation energies and the Hammett correlation, Part 1: Remotely substituted aromatic compounds and vitamin E

AbstractFour hundred and seventy nine experimental values of XZ bond dissociation energies (BDEs) of para‐, ortho‐, meta‐, and multisubstituted aromatic compounds were reproduced by the following simple equations: equation image Here X represents a wide variety of univalent atoms or groups; Y is one or several various remote substituents; and Z represents an oxygen, nitrogen, carbon, or sulfur atom. DH0(XZC5H6) is a known reference/anchor point for a series of XZ bonds. Esr is the remote conjugation energy between the substituents and the reaction center (broken bond), and can be expressed as a Hammett‐type correlation. σ+(Y) is the Brown–Okamoto constant of a substituent Y or the sum of several substituent constants. The Hammett slope or reaction constant ρ is a linear function of the difference between the covalent potentials Vx(Z) and Vx(X). It has been found that equation image and equation image The set of equations are very powerful for the prediction of BDEs, chemical reactivity, and reaction center (or active site) in antioxidants, nutrients, pharmaceuticals, toxicants, carcinogens, and explosives. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 453–466, 2002

Oxidative Damage to and by Cysteine in Proteins: An ab Initio Study of the Radical Structures, C−H, S−H, and C−C Bond Dissociation Energies, and Transition Structures for H Abstraction by Thiyl Radicals

Ab initio computations (B3LYP/6-31G(D), coupled with isodesmic reactions) were used to predict bond dissociation energies (BDEs) of αC−H (DαCH) and other bonds of cysteine, both as free neutral amino acid (AH(Cys)) and as a residue in a model peptide (PH(Cys)). The latter was intended to mimic the environment in proteins. Transition structures were located for intermolecular and intramolecular H atom transfer to a thiyl radical (RS•) from a sulfhydryl group (RSH) or the αC−H bond. The predicted BDEs, at 298 K, in kJ mol-1 to an estimated accuracy of 10 kJ mol-1 for the fully optimized system are (AH(Cys)) DαCH = 322, DβCH = 390, DαCC = 264, and DSH = 373 and (PH(Cys)) DαCH = 346, DβCH = 392, DαCC = 287, and DSH = 367. In PH(Cys) with torsional angles constrained to simulate β-sheet and α-helical secondary structure, DαCH rises to 359 and 376, respectively. Cystine in the peptide environment was modeled by replacing −SH by −SSCH3, PH(CysSCH3), DαCH = 330. Enthalpies of activation for intermolecular H trans...

Prediction of bond dissociation energies using neural network, statistical, and quantum mechanical approaches

Bond dissociation energies (BDEs) are extremely important in chemistry. However, they are notoriously difficult to calculate accurately using quantum mechanical (QM) techniques. Therefore, an alternative that gives similar accuracy to correlated QM techniques, but requires reduced computer time and resources, would be very useful for describing diverse chemical systems. Oxos provide a large library of experimental BDE data with which to assess the potential of different computational methods. Neural network, multiple linear regression, and multiconfiguration self-consistent field calculations are compared. A neural network outperforms MCSCF quantum calculations by a factor of 2.5 in prediction of BDEs for 52 element-oxos, incorporating main group, transition, lanthanide and actinide metal elements. The average absolute difference versus experiment is approximately 12.5 kcal mol −1 for neural network methods versus 28.4 kcal mol −1 for MCSCF calculations.

Prediction of bond dissociation energies and transition state barriers by a modified complete basis set model chemistry

The complete basis set model chemistries CBS-4 and CBS-q were modified using density functional theory for the geometry optimization step of these methods. The accuracy of predicted bond dissociation energies and transition state barrier heights was investigated based on geometry optimizations using the B3LYP functional with basis set sizes ranging from 3-21G(d,p) to 6-311G(d,p). Transition state barrier heights can be obtained at CBS-q with B3LYP/6-31G(d,p) geometries with rms error of 1.7 kcal/mol within a test set of ten transition state species. The method should be applicable to molecules with up to eight or more heavy atoms. Use of B3LYP/6-311G(d,p) for geometry optimizations leads to further improvement of CBS-q barrier heights with a rms error of 1.4 kcal/mol. For reference, the CBS-QCI/APNO model chemistry was evaluated and is shown to provide very reliable predictions of barrier heights (rms error=1.0 kcal/mol).

Toward Site Specificity of Oxidative Damage in Proteins: C−H and C−C Bond Dissociation Energies and Reduction Potentials of the Radicals of Alanine, Serine, and Threonine ResiduesAn ab Initio Study

High-level ab initio computations were used to characterize the parent species and αC radicals for alanine, serine, and threonine, both as free neutral amino acids (AH) and as residues in model peptides (PH) intended to mimic the midchain environment in proteins. The ab initio energies were used in isodesmic reactions to predict bond dissociation energies (BDEs, DαCH) at 298 K, in kJ mol-1, to an estimated accuracy of ±10 kJ mol-1. For the fully optimized systems the values of DαCH are AH(Gly), 331; AH(Ala), 317; AH(Ser), 327; AH(Thr), 328; PH(Gly), 348; PH(Ala), 344; PH(Ser), 348; PH(Thr), 356. All of the DαCH values are less than the BDE of a typical SH bond (370 kJ mol-1), as in cysteine or glutathione (GSH), a result that suggests that oxidative damage at the αC site will not be repaired efficiently by the mechanism of H donation from GSH. Values of DαCH in typical peptide conformations, such as β-sheet and α-helical secondary structure, were estimated by constraining the Ramachandran dihedral angles,...

Calculation of bond dissociation energies for oxygen containing molecules by ab initio and density functional theory methods

Two ab initio (ROHF and MP2), one local (SVWN), four hybrid (BHandH, BHandHLYP, Becke3LYP, and Becke3P86), and two nonlocal (BLYP and BP86) density functional theory (DFT) methods are used for calculating the dissociation energies of molecules that contain H(SINGLE BOND)O, O(SINGLE BOND)O and O(SINGLE BOND)C bonds. The sensitivity to the basis set of the prediction of bond dissociation energies with DFT methods was tested with Becke3LYP on the H(SINGLE BOND)O dissociation energy of water. The 6–31 + G(d) methods are chosen as the smallest basis set which produces reasonable results. The calculated values for all other ab initio and DFT methods were performed with these basis sets and then compared with the experimental data. The suitability of DFT methods for computing reliable bond dissociation energies of oxygen containing molecules is discussed. © 1996 John Wiley & Sons, Inc.

ChemInform Abstract: The Prediction of Bond Dissociation Energies for Common Organic Compounds

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

The prediction of bond dissociation energies for common organic compounds

An empirical equation has been developed which reproduces bond dissociation energy (BDE) values for 65 common organic compounds with an average deviation of less than 0.6 kcal mol −1. The equation is ▪ where DH°(R-X) est is the bond strength to be estimated (for R = ethyl, sec-propyl or t-butyl); X is one of a wide variety of substituents; DH°(CH 3-X) obs is the key experimentally measured (CH 3-X) bond strength; m is the number of methyl groups substituted in CH 3; V x is the covalent potential; ΔV nb is the relief of steric strain between non-bonded atoms when the free radical pair is separated. The equation thus takes into account both inductive effects, related to a new scale of electronegativity, and structural effects.

Density functional Gaussian-type-orbital approach to molecular geometries, vibrations, and reaction energies

We present the theory, computational implementation, and applications of a density functional Gaussian-type-orbital approach called DGauss. For a range of typical organic and small inorganic molecules, it is found that this approach results in equilibrium geometries, vibrational frequencies, bond dissociation energies, and reaction energies that are in many cases significantly closer to experiment than those obtained with Hartree–Fock theory. On the local spin density functional level, DGauss predicts equilibrium bond lengths within about 0.02 Å or better compared with experiment, bond angles, and dihedral angles to within 1–2°, and vibrational frequencies within about 3%–5%. While Hartree–Fock optimized basis sets such as the 6-31 G** set can be used in DGauss calculations to give good geometries, the accurate prediction of reaction energies requires the use of density functional optimized Gaussian-type basis sets. Nonlocal corrections as proposed by Becke and Perdew for the exchange and correlation energies are found to be essential in order to predict bond dissociation energies and reaction energies within a few kcal/mol. The computational efficiency of the present method together with its accuracy, which is comparable to correlated Hartree–Fock based methods, promises a great usefulness of the DGauss approach for the study of large and complex molecular structures.

Dissociative Thermal Electron Attachment to Some Aliphatic Chloro, Bromo, Iodo Compounds

Thermal electron attachment to several aliphatic fluoro, chloro, and bromo derivatives have been investigated in the range 30°–220°C and activation energies of 0–12 kcal have been determined. The relationship between the energy of activation (E*) and change in internal energy (ΔE) for the dissociative electron attachment reaction is uniquely linear with approximately a unit slope. Both chloro and bromo compounds apparently satisfy the same relationship. This empirical relationship can be used to predict bond dissociation energies for aliphatic chloro, bromo, and iodo compounds from the energy of activation for thermal electron attachment. Bond dissociation energies for 1,3-dichloropropane, 1,2-dibromoethane, and 1,3-dibromopropane have been so determined as 75.6, 69.8, 70.9 kcal/mole, respectively. An expression for a two-dimensional representation of the potential-energy curve for the negative ion is proposed with which the linear relationship between E* and ΔE can be derived. The proposed potential-energy curve is empirical, but contains only a single adjustable parameter characteristic of each compound.