Describes and discusses the use of theoretical models as an alternative to experiment in making accurate predictions of chemical phenomena. Addresses the formulation of theoretical molecular orbital models starting from quantum mechanics, and compares them to experimental results. Draws on a series of models that have already received widespread application and are available for new applications. A new and powerful research tool for the practicing experimental chemist.

AB INITIO Molecular Orbital Theory

A new hybrid density functional for general chemistry applications is proposed. It is based on a mixing of standard generalized gradient approximations GGAs for exchange by Becke B and for correlation by Lee, Yang, and Parr LYP with Hartree-Fock HF exchange and a perturbative second-order correlation part PT2 that is obtained from the Kohn-Sham GGA orbitals and eigenvalues. This virtual orbital-dependent functional contains only two global parameters that describe the mixture of HF and GGA exchange ax and of the PT2 and GGA correlation c, respectively. The parameters are obtained in a least-squares-fit procedure to the G2/97 set of heat of formations. Opposed to conventional hybrid functionals, the optimum ax is found to be quite large 53% with c=27% which at least in part explains the success for many problematic molecular systems compared to conventional approaches. The performance of the new functional termed B2-PLYP is assessed by the G2/97 standard benchmark set, a second test suite of atoms, molecules, and reactions that are considered as electronically very difficult including transition-metal compounds, weakly bonded complexes, and reaction barriers and comparisons with other hybrid functionals of GGA and meta-GGA types. According to many realistic tests, B2-PLYP can be regarded as the best general purpose density functional for molecules e.g., a mean absolute deviation for the two test sets of only 1.8 and 3.2 kcal/mol compared to about 3 and 5 kcal/mol, respectively, for the best other density functionals. Very importantly, also the maximum and minium errors outliers are strongly reduced by about 10‐20 kcal/mol. Furthermore, very good results are obtained for transition state barriers but unlike previous attempts at such a good description, this definitely comes not at the expense of equilibrium properties. Preliminary calculations of the equilibrium bond lengths and harmonic vibrational frequencies for diatomic molecules and transition-metal complexes also show very promising results. The uniformity with which B2-PLYP improves for a wide range of chemical systems emphasizes the need of virtual orbital-dependent terms that describe nonlocal electron correlation in accurate exchange-correlation functionals. From a practical point of view, the new functional seems to be very robust and it is thus suggested as an efficient quantum chemical method of general purpose. © 2006 American Institute of Physics. DOI: 10.1063/1.2148954

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Semiempirical hybrid density functional with perturbative second-order correlation

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

The Halogen Bond

Before we start, we need a working definition for MOPAC. The following description has been used many times to describe MOPAC: MOPAC is a general-purpose, semiempirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semiempirical Hamiltonians MNDO, AM 1, MINDO/3, and MNDOPM3, and combir_es the calculations of vibrational spectra, thermodynamic quantities, isotopic substitution effects, and force constants in a fully integrated program. Elements parameterized at the MNDO level include H, Li, Be, B, C, N, O, F, A1, Si, P, S, C1, Ge, Br, Sn, Hg, Pb, and I; at the PM3 level the elements H, C, N, O, F, A1, Si, P, S, C1, Br, and I are available. Within the electronic part of the calculation, molecular and localized orbitals, excited states up to sextets, chemical bond indices, charges, etc. are computed. Both intrinsic and dynamic reaction coordinates can be calculated. A transition-state location routine and two transition-state optimizing routines are available for studying chemical reactions.

MOPAC: A semiempirical molecular orbital program

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, 18F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in po...

Applications of Fluorine in Medicinal Chemistry

Electron diffraction patterns of the fullerene C 60 in the gaseous state have been obtained by volatilizing it from a newly designed oven-nozzle at 730°C. The many peaks of the experimental radial distribution curve calculated from the scattered intensity are completely consistent with icosahedral symmetry for the free molecule. On the basis of this symmetry assumption, least-squares refinement of a model incorporating all possible interatomic distances led to the values r g (C 1 -C 2 ) = 1.458(6) angstroms (A) for the thermal average bond length within the five-member ring (that is, for the bond fusing five- and six-member rings) and r g (C 1 -C 6 ) = 1.401(10) A for that connecting five-member rings (the bond fusing six-member rings). The weighted average of the two bond lengths and the difference between them are the values 1.439(2) A and 0.057(6) A, respectively. The diameter of the icosahedral sphere is 7.113(10) A. The uncertainties in parentheses are estimated 2σ values.

https://science.sciencemag.org/content/sci/254/5030/410.full.pdf

Bond lengths in free molecules of buckminsterfullerene, c60, from gas-phase electron diffraction.

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The Molecular Structure of Disiloxane, (SiH3)2O.

A gaseous electron‐diffraction investigation of SOF4 has led to the discovery of four models in excellent agreement with experiment, all with molecular symmetry C2υ corresponding to replacement of an equatorial fluorine atom of a trigonal bipyramid with oxygen. The models differ largely in the relative magnitudes of the F(eq)···F(eq) and F(eq)···O distances and the F(ax)···F(eq) and F(ax)···O distances. The favored model has the following distance (ra), angle, and root‐mean‐square amplitude (la) values (parenthesized errors are 2σ): S=O=1.403 A (0.0032), S–F(eq) = 1.552 A (0.0043), S–F(ax) = 1.575 A (0.0038), F(eq)···F(eq) = 2.545 A (0.0259), F(ax)···O = 2.121 A (0.0073), F(eq)···O = 2.621 A (0.0139), F(ax)···F(eq) = 2.204 A (0.0050), F(ax)··· = 3.150 A (0.0076), ∠F(eq)SF(eq) = 110.17°(1.82), ∠F(ax)SO = 90.65°(0.42), ∠F(ax)SF(eq) = 89.63°(0.24), ∠F(eq)SO = 124.91°(0.92), lS = O = 0.0367A (0.0050), lS–F(eq) = lS–F(ax) = 0.0540A (0.0029), lF(eq)...F(eq) = 0.0468A (0.0124), lF(ax)...O = 0.0431A (0.0055), lF(...

Kenneth Hedberg

Papers

Bond lengths in free molecules of buckminsterfullerene, c60, from gas-phase electron diffraction.

The Molecular Structure of Disiloxane, (SiH3)2O.

Molecular Structure of Thionyltetrafluoride, SOF4

Least‐squares refinement of molecular structures from gaseous electron‐diffraction sector‐microphotometer data. III. Refinement of cyclopropane

The Molecular Structure of Trisilylamine (SiH3)3N1,2