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Current
Organic Chemistry
ISSN: 1385-2728
Current Organic
Chemistry
Volume 10, Number 7, May 2006
Contents
Theoretical Organic Chemistry
Guest Editors: Qing-Xiang Guo and Lei Liu
Editorial Pp.
693
Theoretical Studies on Chiral Discrimination Pp.
695-714
Ibon Alkorta, Óscar Picazo and José Elguero
[Abstract]
Molecular Modeling and Cyclodextrins: A Relationship
Strengthened by Complexes Pp. 715-729
E. A. Castro and D. A. J. Barbiric
[Abstract]
Computational Studies on Two Supramolecular Structures:
Cyclodextrins and Rotaxanes Pp. 731-743
Carlos Jaime and Miguel de Federico
[Abstract]
Magnitude and Physical Origin of Intermolecular Interactions
of Aromatic Molecules: Recent Progress of Computational Studies
Pp. 745-762
S. Tsuzuki and T. Uchimaru
[Abstract]
Theory of Substituent Effects: Recent Advances
Pp. 763-778
O. Exner and S. Böhm
[Abstract]
Intramolecular Electron Transfer: Computational Study
Based on the Orbital Deletion Procedure (ODP) Pp.
779-790
Yirong Mo
[Abstract]
Studies of Neutral Rare-Gas Compounds and their Non-Covalent
Interactions with Other Molecules Pp. 791-803
Sean A. C. McDowell
[Abstract]
Theoretical Studies on the Ring Opening of β-Lactams:
Processes in Solution and in Enzymatic Media Pp.
805-821
R. López, M. I. Menéndez, N. Díaz,
D. Suárez, P. Campomanes, D. Ardura and T. L. Sordo
[Abstract]
Abstracts
[Back to top]
Editorial
This issue is about theoretical organic chemistry, a versatile
discipline that has contributed considerably to the understanding
of how organic molecules react. It is our greatest pleasure
to share with the readers the wonderful reviews by some of
the eminent scientists in this field.
The interesting chemistry of rare-gas containing organic
molecules is reviewed by Prof. McDowell from University of
Cambridge, England. The recent advances about the theory of
substituent effects are reviewed by Prof. Exner and Prof.
Böhm from Czech Republic. Prof. Mo from Western Michigan
University of USA has reviewed the orbital deletion procedure
and its application to intramolecular electron transfer of
organic compounds.
Prof. Tsuzuki and co-workers from National Institute of Advanced
Industrial Science and Technology of Japan have reviewed the
advances about the intermolecular interactions (π/π,
OH/π,
NH/π
and cation/π
interactions) of aromatic molecules. Prof. Alkorta and co-workers
from Instituto de Química Médica at Madrid have
reviewed the theoretical studies on chiral discrimination.
The exciting chemistry of supramolecular structures such
as rotaxanes is reviewed by Prof. Jaime and co-workers from
Universitat Autònoma de Barcelona. Prof. Castro and
co-workers from Argentina have reviewed the molecular modeling
studies of cyclodextrin complexes. Finally, Prof. Sordo and
co-workers from Spain have reviewed the theoretical studies
on ring opening chemistry of β-lactams
in solution and in enzymatic media.
Qing-Xiang Guo and Lei Liu
Department of Chemistry
University of Science and Technology of China
Hefei 230026
P. R. China
[Back to top]
Theoretical Studies on Chiral Discrimination
Ibon Alkorta, Óscar Picazo and José Elguero
This review summarizes a literature survey on chiral recognition
as viewed from a theoretical point. Nevertheless, experimental
results in the gas-phase are reported when they are relevant
for the theoretical calculations. The review is divided into
the following sections: general considerations, experiment
vs. theory; pure theoretical results; solvent effects; metals
as glue; optical rotatory power, and conclusions.
[Back to top]
Molecular Modeling and Cyclodextrins: A Relationship
Strengthened by Complexes
E. A. Castro and D. A. J. Barbiric
This review deals with the panorama of current theoretical
methods applied to study chemical and physical chemistry properties
of cyclodextrins and their inclusion complexes. This study
covers from 1998 to the present, with the exception of some
papers not included in a rather recent review.
[Back to top]
Computational Studies on Two Supramolecular Structures:
Cyclodextrins and Rotaxanes
Carlos Jaime and Miguel de Federico
Supramolecular structures are formed by holding two or more
molecules without covalent bonds. Although rotaxanes are not
supramolecular species but real molecules, the interactions
existing between the fragments composing rotaxanes are of
the same type of those in supramolecular species. Rotaxanes
and cyclodextrins are the two structures being considered
in this review. The contribution of the authors in the study
of these two classes of compounds by computational techniques
will be presented. Aspects like geometry of the complex (bimodality),
estimation of association constants, conformational changes
produced by the complexation, enantiodifferentiation, changes
in the molecular reactivity, formation of aggregates, shuttling
of the rotaxanes, and the energetic aspects and the geometry
of cyclodiastereomeric rotaxanes are also discussed.
[Back to top]
Magnitude and Physical Origin of Intermolecular Interactions
of Aromatic Molecules: Recent Progress of Computational Studies
S. Tsuzuki and T. Uchimaru
Intermolecular interactions of aromatic molecules (π/π,
OH/π,
NH/π
and cation/π
interactions) are important in many fields of chemistry and
biology. These interactions are important for crystal structures,
stability of biological systems and their molecular recognition
processes. Detailed information on the interactions of aromatic
molecules is essential for improved material and drug design.
However it is not an easy task to study the magnitude and
physical origin of these interactions by experimental measurements
only. Recent developments of computational methodologies and
increasing computer performance enable us to study these interactions
quatitatively by high-level ab initio molecular orbital calculations.
High-level ab initio calculations are rapidly increasing our
knowledge on the intermolecular interactions of aromatic molecules.
This review attempts to introduce methodologies for studying
weak intermolecular interactions by ab initio calculations
and to summarize recent progress in quantitative analysis
of intermolecular interactions of aromatic molecules.
[Back to top]
Theory of Substituent Effects: Recent Advances
O. Exner and S. Böhm
The review reports recent progress in the studies of substituent
effects in isolated molecules, i. e. based either on the experimental
gas-phase acidities (basicities), or on quantum chemical calculations.
Attention was focused on cases when the results differed from
or exceeded the traditional views: redefinition of the inductive
effect, quantitative estimation of resonance, validity of
the Hammett equation, interpretation of the ortho effect,
additivity of the enthalpies of formation, acidity of carboxylic
acids.
[Back to top]
Intramolecular Electron Transfer: Computational Study
Based on the Orbital Deletion Procedure (ODP)
Yirong Mo
The elucidation of the molecular structure-property relationships
requires the rational estimation of steric and electronic
effects which govern the molecular structures. To this end,
we proposed a simple ab initio method called orbital deletion
procedure (ODP) which can quantitatively probe the intramolecular
electron transfer effect in carbocations and boranes. This
method can not only explore the impact of electron transfer
on molecular structures and stabilities, but probe the electron
transfer efficiency in some electron donor-bridge-electron
acceptor (DBA) complexes. In this Review, we will demonstrate
the significance of the intramolecular steric effect by comparing
the planar and staggered structures of tetrahydrodiboron (B2H4)
and halogenated diboranes (B2X4,
X = F, Cl, Br). By deactivating the electronic effect, we
found that in these systems the staggered structures are consistently
stabilized by 4-11 kcal/mol compared with the planar structures,
which supports our very recent conclusion that the ethane
rotation barrier is dominated by the steric hindrance rather
than the hyperconjugative interactions. We further analyzed
a few carbocations and demonstrated how conjugation or hyperconjugation
can remarkably influence the molecular structures and properties.
Based on the ODP method, we proposed a two-state model which
can straightforwardly compute the electron-transfer matrix
element which is directly related to the electron transfer
efficiency and kinetics in H2C-bridge-CH2+
DBA complexes. We employed this ODP-based two-state model
to investigate the electron transport across strain-free linear
alkyl chains (CH2)n
(n=1-8) and linear π-conjugated
bridges (CH=CH)n
(n=1-5).
[Back to top]
Studies of Neutral Rare-Gas Compounds and their Non-Covalent
Interactions with Other Molecules
Sean A. C. McDowell
The main focus of this review is a new class of neutral molecules
containing chemically bonded rare gas atoms. These compounds
are given by the general formula HRgX, where Rg denotes a
rare gas atom and X denotes an atom or group of atoms having
high electron affinity. They are usually produced by photolysis
of a HX precursor in low temperature rare-gas matrices. These
novel compounds are highly polar and form weakly bound metastable
complexes with other molecules via non-covalent interactions.
In this review, we discuss theoretical studies of the structure,
bonding, properties and factors influencing the energetic
stability of these rare-gas species, the preparation and vibrational
spectroscopy of these molecules and some theoretical approaches
to understanding the nature of these molecules, with experimental
studies discussed where appropriate. The complexes formed
by the rare-gas compounds exhibit unusual structural and spectroscopic
features, which are also discussed in the review.
[Back to top]
Theoretical Studies on the Ring Opening of β-Lactams:
Processes in Solution and in Enzymatic Media
R. López, M. I. Menéndez, N. Díaz,
D. Suárez, P. Campomanes, D. Ardura and T. L. Sordo
Herein we present an overview of the theoretical studies on
the cleavage of the β-lactam
C-N bond in aqueous solution and in enzymatic media. We discuss
first the alkaline hydrolysis of β-lactams
that has been investigated thoroughly by means of semiempirical,
ab initio, and density functional calculations, while solvent
effects have been typically included using a discrete and/or
continuum representation of solvent. These computational studies
investigate the origin of the energy barrier, the structure
and stability of tetrahedral intermediates, substituent effects,
catalysis by transition metals such as Zn(II) and Cu(II),
etc. Other recent articles have been devoted to the analysis
of the acidic and neutral hydrolysis/alcoholysis of β-lactams
as well as their ozonolysis. We also review a series of theoretical
studies that describe the ammonolysis/aminolysis of monocyclic
and bicyclic β-lactams
using density functional calculations combined with a solvent
continuum model. The aminolysis reaction between the lysine
199 residue of Human Serum Albumin and benzylpenicillin is
also revised. The second part of this review concentrates
on the β-lactam
ring opening catalyzed by the “penicillin recognizing
proteins” family of bacterial enzymes, which includes
both serine-proteases and zinc-proteases. For the serine proteases
(β-lactamases
and penicillin binding proteins), quantum chemical optimizations
on cluster models of their active sites and hybrid quantum
chemical and molecular mechanical calculations on the whole
enzymes, have been applied to examine several competing mechanisms
that differ in the identity of the required base to activate
the nucleophilic serine. For the zinc-β-lactamases,
the gross of computational work has been aimed at examining
the coordination chemistry of the catalytic metal centers,
and only a few mechanistic studies have been reported to date.
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