Vernon G.S. Box

City College of New York | CCNY · Department of Chemistry

We often associate the conjugation of p-bonds with an automatic delocalization of p-electron density. This incorrect idea can hide some of the more interesting aspects of conjugated p-electron systems. The X-ray crystallographic structural analyses of a number of simple, but representative molecules, rather than a speculative theoretical review, sh...

The well known "propeller-like", structures of the triarylmethyl (trityl) carbocation and the simple derivatives show dihedral angles of about 30 degrees between the "aryl ring blades" and the "central carbocationic hub".[1] This large dihedral angle ought to have precluded any resonance between the aromatic rings and the central cation, however mo...

The study of the crystallographic data for peroxides prompted a review of the diffraction data and bond lengths or molecules having the structure (H) n-X-O-H. While hydroxylamine has already been discussed, some of the intriguing chemistry of the (H) n-SO -H and (H) n-P-O-H molecules need to be reviewed.

A review of the mechanism of the hydrolyses of acetals and orthoesters has forced us to review the validity, and usefulness, of the notion of n-s* interactions in orthoesters, glycopyranoses and glycopyranosides.

Increasingly, the question of what kind(s) of orbitals the lone pairs of electrons of a simple ether oxygen are "found" in, is being debated. The X-ray diffraction data of a range of oxygen-containing molecules can clearly answer this question. One suspects that the rigid adherence of the Molecular Orbital (MO) theoreticians to a s/p pair might be...

The crystallographic structures of congested amines, their carboxamides, and the carboxamides of the common azaheteroaromatic molecules, reveal several inconsistencies with their molecular orbital theory predicted structures. These molecules force us to reexamine our normal understanding of their nitrogen atom's lone pair of electrons.

Pyridines, pyrazines, pyrimidines, pyrroles and imidazoles are undoubtedly aromatic molecules. Their C=C and C=N bond orders are consistently close to 1.7 and their bond lengths are consistently close to those predicted for their delocalized analogues. Unsurprisingly, therefore, many chemists assume that their other polyaza-analogues will be aromat...

Azulene stands out from the other small aromatic molecules because of its charming blue colour and its measurable dipole moment. It's immediate isomeric aromatic neighbour, naphthalene, is colourless and is non-polar. These facts immediately raise questions about the possible differences in the p-electron delocalization found in these two molecules...

Molecular Orbital and VSEPR theories have successfully helped organic chemists to understand covalent bonding by the elements of the first three periods of the periodic table. A similar pragmatic approach can help us to understand bonding in the transition metal complexes, especially since we can never fully rationalize the orbitals of the transiti...

The relationship between the covalent radius and bond type for the elements of the first three periods, from hydrogen to argon, has been firmly established and is taught to beginning chemistry students. The covalent radii of these atoms have been used to predict not only the types of their bonds, but also their lengths. Metal atoms, however, presen...

The X-ray crystallographic diffraction data from some common salts strongly suggest that one electron covalent bonding is the norm in the unit cells of all crystalline salts. The assumption that these unit cells simply contained independent, hard-sphere-like, ions is incorrect. Estimating ionic radii from unit cell measurements can be highly mislea...

StruMM3D - {Str3Di32 and QVBMM} - A Molecular Mechanics powered, 3-Dimensional Molecular Graphics and Molecular Modeling Tool for Organic Chemists, Organometallic Chemists and Crystallographers

Many Quantum Mechanics and Molecular Orbital theoreticians insist that all conjugated p-systems, especially coplanar ones, must be delocalized. This fallacy is highlighted in reviewing the X-ray crystal structures of several nitrophenols, aryl nitro-compounds, and other molecules. Extremist views among quantum chemistry theoreticians about indefini...

It is generally understood that a calculated Pauling bond order, of a selected bond, infers the multiplicity of the bond and hence the electron density in that bond. This interpretation is incorrect and has generated many fallacies in the chemistries of covalent molecules.

The X-ray crystallographic data for a large group of ferrocenes have revealed that the central iron atoms are in their Fe(III) state, as is found in their ferricenium ions.

Only a few molecules have stimulated the discussion and understanding of reaction mechanisms in organic chemistry. as has the 2-norbornyl Carbocation. New structural evidence has shed more light on this enigma.

Valence Shell Electron Repulsion (VSEPR) Theory is widely taught and utilized in organic chemistry, and is probably the most reliable simple method for predicting gross molecular structures. The attempt to quantify some aspects of VSEPR Theory, in the creation of the molecular modeling program StruMM3D, has uncovered some interesting flaws in VSEPR...

A careful examination of the x-ray crystallographic data for triphenylphosphine, some of its simple derivatives, and tetrakis(triphenylphosphine)palladium(0) suggests that the currently held views on the bonding features of tetrakis(triphenylphosphine)palladium(0) are incorrect.

It is generally understood that a calculated Pauling bond order, of a selected bond, infers the multiplicity of the bond and hence the electron density in that bond. This interpretation is incorrect and has generated many fallacies in the chemistries of covalent molecules.

A 25 years long empirical study of bond lengths and their relationship to bond types, in molecular structures determined by x-ray crystallography, has shown that bond lengths are very closely tied to bond types and that the bond length ranges that correspond to the different bond types do not overlap. Thus, there is no validity to assigning fractio...

π-Εlectron delocalization exerts one of the most significant structure or energy influences in organic chemistry. Apart from determining the shapes of alkenes and alkynes, the planarity of aromatic molecules is a hallmark of π-electron delocalization. Huckel’s rules for aromaticity are easily applied in the teaching of undergraduates, but occasiona...

ChemInform 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 molecular modeling program STR3DI32.EXE and its molecular mechanics module quantized valence bonds' molecular mechanics (QVBMM) were used to simulate the stereo-electronic effects present in the conformers of 2-hydroxypyran, 2-methoxypyran and the 1,8-dioxadecalins in order to evaluate the relative energies and hence nucleophilicities of their...

ChemInform 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.

ChemInform 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.

ChemInform 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.

ChemInform 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.

ChemInform 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.

A 25 years long empirical study of bond lengths and their relationship to bond types, in molecular structures determined by x-ray crystallography, has shown that bond lengths are very closely tied to bond types and that the bond length ranges that correspond to the different bond types do not overlap. Thus, there is no validity to assigning fractio...

While exploring the stereochemistry of the di-and trihalocyclohexanes, using the Molecular Mechanics based program StruMM3D, we encountered a series of cyclohexanoid molecules in which dipolar interactions overrode the normal equatorial conformational preferences for some substituents. Similar effects had also been encountered in the 2-halocyclohex...

Some of the more potent, and interesting, natural products that have marked biocidal properties have one, or more, amide functional groups. On the other hand, there are countless amides that are non-toxic. Thus, there is a need to try to identify the structural features of biocidal amides that could indicate their potential toxicity. A review of th...

A variety of molecules bind to DNA in its major and minor grooves, and some, like the anthraquinoids, are known to form intercalates in which these molecules are inserted directly into the double helix, between the bases. Several researchers have pointed to an electron transfer mechanism (leading to ion pairing) as one of the factors that could hol...

Considerable attention has been focused on the DNA double helix, especially on the properties of its nucleotidic bases, but little attention has been paid to the role of the 2-deoxyribosyl moiety. The available computer-assisted theoretical methods have not been entirely helpful in enabling researchers to identify new stereo-electronic interactions...

The stereochemical features of the dihaloethanes and the dihalocyclohexanes have attracted significant attention over the years. While the dichloro- and the dibromo-compounds seem to display the stereochemical preferences that we would normally predict for them, the analogous difluorocompounds do not. More specifically, the 1,2-difluorocompounds se...

The X-ray crystallographic coordinate data of a 56 DNA double helical oligomers were examined, using the molecular modeling program STR3DI32.EXE, in order to ascertain the aromatic statuses of the Watson-Crick hydrogen bonded base pairs. Several oligomers that were intercalated with anthraquinoid molecules (like the daunomycin and nogalamycin aglyc...

1,3-Dioxole has been shown to be non-planar by infrared and Raman spectroscopy. An MM3 study of this molecule enabled the investigators to suggest that this non-planarity was due to the anomeric effect. Subsequently, an ab initio theoretical study of this molecule was performed, which also concluded that the non-planarity of 1,3-dioxole was due to...

The molecular modeling program STR3DI32.EXE and its molecular mechanics module quantized valence bonds' molecular mechanics (QVBMM) were used to simulate the stereo-electronic effects present in the conformers of 2-hydroxypyran, 2-methoxypyran and the 1,8-dioxadecalins in order to evaluate the relative energies and hence nucleophilicities of their...

An efficient synthesis of 1-O-pivaloyl-4-O-(2-methoxybenzyl)-3,6-anhydro-α-D-mannopyranose from methyl α-D-glucopyranoside has been developed. The glycosidic hydrolysis of methyl 2-O-pivaloyl-4-O-(2-methoxybenzyl)-3,6-anhydro-α-D-mannopyranoside was accompanied by an unusual ester migration of the pivalate group to C-1. Molecular modeling, using ST...

The molecular modeling program STR3DI32.EXE, and its molecular mechanics module, QVBMM, were used to simulate and evaluate the stereo-electronic effects in the pyranoid analogs of the derivatives of monosaccharides that are known to display the reverse anomeric effect. This study has confirmed the importance of bond dipoles, particularly hydrogen b...

A molecular modeling review of the X-ray crystallographically determined structures of some proteins and polypeptides, from the Brookhaven Protein Data Bank, has enabled us to identify chemically reactive, weak, amidic linkages in some of these molecules. This discovery should add new dimensions to the discussion of the significance of the tertiary...

The molecular modeling program STR3DI.EXE, and its molecular mechanics module, QVBMM, were used to simulate, and evaluate, the stereo-electronic effects in the mono-alkoxides of the 4,6-O-ethylideneglycopyranosides of allose, mannose, galactose and glucose. This study has confirmed the ability of these molecular modeling tools to predict the regioc...

Abstract - There are many old misconceptions in our currently used textbooks, particularly those used by undergraduates. Several of these misconceptions involve the structural features of molecules that cannot easily be observed experimentally, and so have remained, unchallenged, through the years. Molecular modeling is a reliable method for debunk...

Aromatic aldehydes, ketones and acylbenzo[b]furans have been reductively deoxygenated with sodium cyanoborohydride and the mild electrophile chlorotrimethylsilane.

The new force field, Quantized Valence Bonds' Molecular Mechanics, QVBMM, was designed to embrace most of the concepts in Valence Shell Electron Pair Repulsion (VSEPR) theory and to uniquely integrate lone pairs into molecular mechanics. This force field is executed in the molecular modeling program STR3DI.EXE and is particularly useful in the mole...

The newly developed Quantized Valence Bonds' Molecular Mechanics (QVBMM) force field, which is implemented in the STR3DI molecular Modeling program, is an excellent tool for the simulations of the structures and reactivities of the saccharides. The QVBMM force field has already allowed us to enhance our understanding of the anomeric effects, and co...

Molecular modeling can provide great stimulation to the pedagogical process if students and teachers use this tool to examine the structural aspects of organic molecules whose structures have been determined by X-ray crystallography. An example of this is provided by one of our undergraduate research projects that examined delocalization in p-syste...

A new force field, Quantized Valence Bonds' Molecular Mechanics (QVBMM) has been included in the molecular modeling program STR3DI.EXE. The QVBMM force field successfully embraces and implements all of the pivotal concepts in VSEPR theory and uniquely integrates lone pairs into molecular mechanics. QVBMM facilitates a detailed analysis of the stere...

The formation of oxonium ions during the acid catalyzed reactions of the tricyclic eudesmanoid orthoesters (3) and (4) is greatly influenced by the overall structural features of the parent molecules. The structures of the reaction products, and molecular modeling of the possible oxonium ions, confirm that the most stable oxonium ion is the most im...

New criteria (based on X-ray crystallographic data) for assessing the presence of delocalization in conjugated π systems reveal that delocalization is not a widespread phenomenon in the ground states of many of these π systems. Instead, these molecules prefer to retain highly localized, independent, π systems. Thus, many explanations of the structu...

128. Keywords (Domain): Organic Chemistry

A synthesis of allylsilanes from lactones and protected hydroxy esters is reported. These allylsilanes were converted into novel oxygen heterocyclic compounds.

ChemInform 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.

Birch reduction of the methoxyphthalides (I) in the presence of ammonium acetate as the proton donor and subsequent alkylation with 1,2-dibromopropene (II) yield the (bromoallyl)methoxydihydrophthalides (III) which form the fused cyclohexenones (IV) upon acidic hydrolysis.

ChemInform 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 first successful reductions of the aromatic rings of phthalides, with the preservation of the lactone rings, are reported. The reduction/alkylation of some substituted 4-methoxyphthalides gave lactonic enol ethers, which were converted into conjugated homocyclic dienes and further into cyclohexenones. These enones were easily converted into bic...

Die Stereoselektivität in der Claisen-Umlagerung vdn Pyranosiden und entsprechenden Carbocyclen wird an zahlreichen Verbindungen untersucht.

Structurally equivalent derivatives of pyranosides and cyclohexanes undergo the spiro-Claisen rearrangement with different stereochemical results. A rationalization for the course observed with the pyranosides is suggested, which invokes interaction of the oxygen lone pair with a (developing) electron deficient centre at the spiro carbon.

Aus dem methylverzweigten Glucosid (II) kann durch Oxidation das Methylthiomethylether-Keton ( l) oder das Hydroxyketon (III) erhalten werden.

Unter den im Titel angegebenen Bedingungen können Diole wie das Glycosid (I) selektiv zu (II) monobenzoyliert werden.

The electronic factors which contribute to the anomeric effects have been attributed to the destabilizing n-n (lone pair - lone pair), or/and the stabilizing n-σ*, interactions of the non-bonded electron pairs of geminal heteroatoms. Predictions of the chemistry of the simple monosaccharide acetals, based on a n-σ* hypothesis, are not consistent wi...

Das Verhalten der Cumarine (Ia) und (Ib) in siedendem Diethylanilin (II) wird untersucht.

Der 3-Methylbenzofuran-2 arbonsiitnreester (I) wird zu (II) bromiert und weiter in die Aryloxy-Verbindungen (III) übergeführt, die mit Trifluoressigsiiure (TFA) zu den Phenolen (IV) umgelagert werden.

The preparation of the title compound from methyl 4,6-O-benzylidene-2-C-methyl-2-O-(methylthio)methyl-α-d-ribo-hexopyranosid-3-ulose and its single-crystal X-ray structural characterisation is described. Consistent with the chemistry of methyl 4,6-O-benzylidene-α-d-ribo-hexopyranosid-3-ulose1, the Grignard reduction of the two 2-C-methyl-α-d-ribo-h...

The title compounds were prepared by the acid catalysed rearrangements of some 2-carbethoxy-3-aryloxymethylbenzofurans to the 2-carbethoxy-3-(2′-hydroxyarylmethyl)-benzofurans, followed by their lactonisation. These 2-carbethoxy-3-aryloxymethylbenzofurans do not undergo the Claisen rearrangement.

The esterifications of some 4,6-O-benzylidene-hexopyranosides by the phase transfer method are reviewed and a mechanism for these reactions is proposed which takes into account the differential nucleophilicities of the oxygens, 0-2 and 0-3, as predicted by the β-effect and the γ-effect1. The similarities between the tin mediated esterification and...

Mechanistic proposals are presented which seek to describe the course of the esterification of a 4,6-o-benzylidene-hexopyranoside by an acid chloride or an acid anhydride. These two proposals are then elaborated into a rationalisation of the selectivity observed in the esterification of the hydroxyl groups of some 4.6-o-benzylidene-hexopyranosides....

N,N-diethylaniline effectively debrominated 3-bromo-4-methyl- 7-methoxycoumarin and 3-bromo-4-bromomethyl-7-methoxycoumarin at reflux∗ This and other reactions of the above-mentioned coumarins in refluxing N,N-diethylaniline provided supporting evidence for the mechanism of the fragmentation of simple 4-Aryloxy-2-bromo-but-2-enoates which occurred...

Die Oxidation des Glucosids (I) führt zur Ulose (II) und bei längeren Reaktionszeiten zum Enolester (III).

Aus dem Brommethylcumarin (I) entstehen die Pyridiniumsalze (III).

Die Ulose (I) reagiert mit den Grignard-Verbindungen (II) einheitlich zu den 3-C-alkylverzweigten Zuckerderivaten (III) mit alle-Konfiguration, die zu (IV) acetyliert werden.

An attempt is made to rationalise the elimination and enolisation processes observed in 4,6-O-benzylidenehexopyranosides and hexopyranosiduloses. The roles of the oxygen substituents on the pyran ring are outlined, and it is suggested that these oxygen atoms control the paths of the reactions.

A general synthetic route to the title compounds is outlined which involves: (a) the Grignard reduction of methyl 2-O-benzoyl-4,6-O-benzylidene-α-d-ribo-hexopyranosid-3-ulose; (b) the dehydration of the derived methyl 2-O-acetyl-3-C-alkyl-4,6-O-benzylidene-α-d-allopyranoside, with thionyl chloride-pyridine, at 0°, to provide the methyl 2-O-acetyl-3...

Aus dem Glucosederivat (I) erhält man nach bekannten Methoden das Keton (II), das mit Methylmagnesiumiodid (III) nach Hydrolyse das Diol (IV) liefert.

Das Hydroxycumarin (Ia) wird durch die entsprechenden Benzoylchloride in die Aroyloxycumarine (Ib) und (Ic) übergeführt, die unter Bestrahlung zu den Arylketonen (II) bzw. (III) umgelagert werden.