Concept Of Molecular Structure Research Articles

Laser-induced dynamic alignment of the HD molecule without the Born-Oppenheimer approximation.

Laser-induced molecular alignment is well understood within the framework of the Born-Oppenheimer (BO) approximation. Without the BO approximation, however, the concept of molecular structure is lost, making it hard to precisely define alignment. In this work, we demonstrate the emergence of alignment from the first-ever non-BO quantum dynamics simulations, using the HD molecule exposed to ultrashort laser pulses as a few-body test case. We extract the degree of alignment from the non-BO wave function by means of an operator expressed in terms of pseudo-proton coordinates that mimics the BO-based definition of alignment. The only essential approximation, in addition to the semiclassical electric-dipole approximation for the matter-field interaction, is the choice of time-independent explicitly correlated Gaussian basis functions. We use a variational, electric-field-dependent basis-set construction procedure, which allows us to keep the basis-set dimension low while capturing the main effects of electric polarization on the nuclear and electronic degrees of freedom. The basis-set construction procedure is validated by comparing with virtually exact grid-based simulations for two one-dimensional model systems: laser-driven electron dynamics in a soft attractive Coulomb potential and nuclear rovibrational dynamics in a Morse potential.

Structure, shape, topology: entangled concepts in molecular chemistry

The concepts of molecular structure and molecular shape are ubiquitous in the chemical literature, where they are often taken as synonyms, with unavoidable drawbacks in chemistry teaching. A third concept, molecular topology, is less frequent but it is a reference term in molecular research domains such as Quantitative Structure–Activity Relationships. The present paper proposes an epistemological analysis of these three notions, aimed at clarifying the nature of their relationship, as well as the contiguities and differences between them. At first, we discuss the various acceptations of the terms molecular structure and molecular shape. Then, we examine some crucial milestones in the history of these concepts and we analyse the relationship between structure, shape and topology from an epistemological viewpoint. We point out the distinguishing features of each concept and we show that their semantic openness, that may be fruitful in a specialized context, turns into a source of incoherence and inaccuracy in the teaching context, fostered by the misleading use of these terms made by textbooks. Eventually, we propose a criterion fit to discriminate between the conceptual domains of molecular shape, molecular structure and molecular topology.

Effects of Temperature on the Shape and Symmetry of Molecules and Solids.

Despite its undeniable problems from a philosophical point of view, the concept of molecular structure, with attributes such as shape and symmetry, directly borrowed from the description of macroscopic objects, is nowadays central to most of the chemical sciences. Descriptions such as "the tetrahedral carbon atom" or "octahedral coordination complexes" are widely used as much in elementary textbooks as in the most up-to-date research articles. The definition of molecular shape is, however, not as simple as it might seem at first sight. Molecules don't behave as macroscopic objects do, and the arrangement of atoms within a molecule changes continuously due to the incessant motion of its constituent particles, nuclei, and electrons. How are molecular shape and symmetry affected by this thermal motion? In this Minireview, we introduce the language of continuous symmetry measures as a new tool to quantitatively describe the effects of temperature on molecular shape and symmetry, enriching in this way the set of molecular descriptors that might be used in the establishment of new empirical structure-property relations, of great interest in concomitant areas such as medicinal chemistry or materials science.

Collective Molecular Superrotation: A Model for Extremely Flexible Molecules Applied to Protonated Methane.

The concept of molecular structure is traditionally considered to be virtually fundamental. However, it breaks down in extremely flexible molecules, whose dynamics are governed by large-amplitude motions. For the dynamics of molecules with free internal rotations, we therefore propose a five-dimensional rigid rotor model, with states characterized by two generalized angular momentum quantum numbers and a rotational constant B. The quantum numbers characterize a 5D angular-momentum vector, super-j, which describes collective rotations that involve both the internal and the overall rotation. This model predicts the lowest energy states of the prototypical, extremely flexible molecule, CH_{5}^{+}. Both energies and symmetries compare very favorably to recent experimental results. The respective assignment to the new quantum numbers indicates the validity of our concept of collective rotations in extremely flexible molecules.

ChemInform Abstract: The Woodward Research Institute, Robert Burns Woodward (1917—1979) and Chemistry Behind the Glass Door

AbstractReview: 59 refs.

The Woodward Research Institute, Robert Burns Woodward (1917–1979) and Chemistry behind the Glass Door

AbstractCertainly a highlight in the career of Nobel Laureate Professor Robert Burns Woodward (1917–1979) was the foundation of the Woodward Research Institute (WRI) at Ciba AG in Basel, Switzerland, in 1963. Woodward's remarkable accomplishments in the development of organic chemistry altered not only our concepts of molecular structure, but also our comprehension of physico‐chemical properties. In his legacy, Woodward devised innovative strategies for natural product syntheses based on brilliant rationale of their properties and an uncanny sense of Nature. The chemistry community benefited not only at Harvard but especially in Basel and Zürich from Woodward's inspiring lectures and the opportunity to learn from the chemistry Meister. This article highlights parts of the chemistry and some personalities that contributed to forefront investigations at the Woodward Research Institute which began at the former Novartis legacy company, Ciba AG, Basel.

On the importance of the Born – Oppenheimer approximation in intramolecular dynamics

The concept of molecular structure, fundamental for correctly configuring space in the problem of describing the discrete spectrum of intramolecular dynamics, can be introduced only in the Born-Oppenheimer approximation. Therefore, it is this approximation that allows formalizing the formulation of this problem. The symmetry properties of dynamics give rise to limitations in determining some types of internal motions, whose violation leads to incorrect physical conclusions.

The chemist’s concept of molecular structure

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

What can the activation process model give the adiabatic and non-adiabatic approximation?

In the framework of the adiabatic approach: the notion of a quantum subsystem for a separate molecule has been determined; the mechanism of transition from the previous quantum subsystem to the subsequent one has been offered; the calculation of average energy of high-energy rotational spectral components has been carried out from first principles for the diatomic molecule; the average energy of the translation of Hg and H atoms, participating in the HgH molecule elementary dissociation process, has been estimated; the overall system of equations for the elementary dissociation process of the molecule has been received; the notion of a quantum subsystem for a protein molecule has been defined; on the basis of this definition the kinetics of folding and insertion for the β-barrel outer membrane protein A (OmpA) of Escherichia coli into dioleoylphosphatidylcholine (DOPC) bilayers has been simulated numerically; the possible adequacy of the model to dynamic properties of the protein mobility has been shown. For the non-adiabatic approach: the quantum subsystem notion has been given; the phenomena of IR multi-photon absorption and photodissociation for molecules in the intensive field of laser radiation have been explained; the transcendental equation for calculation of a number of identical IR quanta absorbed by the molecule under its dissociation has been derived from first principles; the estimation of this parameter for the SF 6 molecule has been carried out, and good coincidence with experimental results has been shown. In accordance with the model proposed, the concept of molecular structure has been outlined.

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.

COMPEL is a database on composite regulatory elements, the basic structures of combinatorial regulation. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. The structure of the relational model of COMPEL is determined by the concept of molecular structure and regulatory role of CEs. Based on the set of a particular CE, a program has been developed for searching potential CEs in gene regulatory regions. WWW search and browse routines were developed for COMPEL release 3.0. The COMPEL database equipped with the search and browse tools is available at http://compel.bionet.nsc.ru/. The program for prediction of potential CEs of NFAT type is available at http://compel.bionet.nsc. ru/FunSite.html and http://transfac.gbf.de/dbsearch/funsitep/ s_comp.html

Number Mysticism in Scientific Thinking

For millennia, human beings have been tantalized by the idea that integers and patterns of numbers carry deep hidden meanings. They have searched assiduously for these cryptic insights. Numerological analysis has been embraced ardently in mythology, religion, and the sciences. I want to focus particularly on the fascination with integers during the evolution of concepts of molecular structure and behavior of protein macromolecules, an area in which I have lived for half a century. To place these in a broader perspective, however, I shall start with a sampling of number mysticism in other fields of knowledge. the number corresponding to the name of the former is 1276, and to that of the latter 1225; "obviously," the larger number must be the dominating one. In the middle ages, Jewish Kabalists and Christian theologians developed

Models of 2-Butanone: Using Graphics To Illustrate Complementary Approaches to Molecular Structure and Reactivity

157. Ways in which a graphics workstation can be used to illustrate various concepts of molecular structure.

A fibered space approach to chemical reaction mechanisms

In this article we generalize the necessary conditions for a topological definition of the concept of molecular structure, showing that it may be independent of the particular criterion chosen, as long as it fulfills some general conditions and may give rise to the concept of a category of stable chemical structures. We proceed to introduce a local metric in the objects of this category by using the properties of metric space bundles, and this allows us to propose a general system of reaction mechanisms within this framework of the theory of categories. We conclude by proposing a single diagram that encompasses the whole theory of stable structures and reaction mechanisms. © 1992 John Wiley & Sons, Inc.

The concept of molecular structure in structure–activity relationship studies and drug design

We can justify the use of any model, method, or algorithm if we clearly state our goals, understand the basis of our procedures, and fully appreciate the true nature and limitations of the results. As we have illustrated here, the creation of new wisdom may appear to be a consequence of our labors. There are cases, however, where this creation may be only an illusion. In any analysis of structure-activity, property-activity, or structure-property relationships, the degree of understanding of the nature of the starting data therefore determines the level of confidence ascribable to any result and prediction. This is, in essence, the message of our inquisitive meditations on the deep nature of structure-activity relationships.

Evolution of Bonding Theory: The Werner-Jorgenson Controversy

This simulation introduces general chemistry students to the process by which concepts of molecular structure and bonding developed during the 19th century.

Instability of tunneling and the concept of molecular structure in quantum mechanics: The case of pyramidal molecules and the enantiomer problem.

Instability of tunneling and the concept of molecular structure in quantum mechanics: The case of pyramidal molecules and the enantiomer problem.

On the interplay between theory and experiment in molecular structure problems: Some case studies

AbstractSome brief, general comments on the concept of molecular structure will be given. Some important points connected to the use of models in the interpretation of molecular structures will also be mentioned. The main theme in one part of the presentation will be the cooperative efforts made by experimentalists (mainly spectroscopists) and theoreticians (computational chemists) in order to measure, predict, and analyze the perturbations on the cyclopropane ring by different substituents. The aim is to demonstrate that ab initio calculations of a certain quality can constitute an important support for experimental studies in that they are able to discriminate between different models that otherwise are equally probable. The second part of the presentation will be concerned with a class of molecules that gives both experimental structural chemists and computational chemists a great challenge, namely, the metallocenes. A discussion of some of the grave discrepancies between theory and experiment regarding their geometry will be given.

Molecular defects in interactions of platelets with the vessel wall.

The objectives of this review have been to summarize the recent research on inherited defects involving abnormal platelet function and to illustrate how studies of hemorrhagic syndromes have led to an increased understanding of the molecular events involved in platelet adhesion and aggregation. Emphasis has been placed on the two primary hemostatic reactions: the interaction of platelets with von Willebrand factor to promote adhesion to the subendothelium, and the interaction of platelets with fibrinogen to promote platelet aggregation. Even as these events are more clearly defined, new concepts of molecular structure, function, and heterogeneity are emerging, and the variety of recognized genetic defects is becoming more complex.

The Concept of Molecular Structure in Quantum Theory: Interpretation Problems

AbstractThe classical concept of molecular structure (namely, a set of atoms with a well‐defined geometrical arrangement in space) originated well before the advent of quantum theory, and, contrary to widespread views, these two conceptual schemes (classical molecular structure and quantum theory) are not easy to reconcile. We begin with a preliminary discussion of molecular structure in terms of space and time correlations in the framework of quantum theory. Then we summarize the salient features of some critical views raised‐during recent years (essentially by Woolley) concerning the concept of molecular structure. The essential claim of this viewpoint is that “molecular structure” is not an intrinsic attribute of an isolated molecule, and appears rather as an effect of the environment (other molecules? vacuum electromagnetic field, according to quantum electrodynamics?). Afterwards, we discuss these issues in detail: we show that it is necessary to distinguish between a “quantum” or “potential” structure (which may be deduced in a straightforward way from the quantum treatment of the molecule), and the “classical” molecular structure (according to which the molecule is considered as a set of rotating and vibrating material points, corresponding to the atoms); we briefly discuss some aspects of the Born–Oppenheimer approximation. From our discussion, we deduce that the “classical structure” concept is indeed non‐trivial from a purely quantum‐mechanical point of view; in actual fact, it is related to the problem of the “classical limit” of quantum mechanics, and it appears that, at the present time, none of these classical concepts and behaviours is convincingly derivable from a strict quantum mechanical basis. Finally, we consider these same problems from the point of view of stochastic electrodynamics (SED), which is one of the stochastic models for microphysics proposed so far as a possible alternative or extension of usual quantum theory. In the framework of such a theory, the “classical limit” and, in particular, the “classical molecular structure” no longer poses a problem, but aside from these satisfactory qualitative aspects, several quantitative failures of SED prevent us from accepting it, at least in its present state, as a genuine physical alternative to quantum theory. We therefore conclude that “classical molecular structure”, and classical concepts in general, remain an open problem in the framework of present‐day quantum physics.

Ab initio studies of molecules and concepts of molecular structure

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb initio studies of molecules and concepts of molecular structureJerry L. WhittenCite this: Acc. Chem. Res. 1973, 6, 7, 238–245Publication Date (Print):July 1, 1973Publication History Published online1 May 2002Published inissue 1 July 1973https://doi.org/10.1021/ar50067a004RIGHTS & PERMISSIONSArticle Views75Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1022 KB) Get e-Alerts Get e-Alerts