Rozprawy doktorskie na temat „Weakly Bound Molecules”

This thesis is concerned with the computational simulation of weakly bound molecules. Two general methods of producing potential energy surfaces, Neural Networks and Gaussian processes, are described and evaluated. The Neural Network method is used to generate potential functions for HF-HCI, H₂-HF and H₂-HCI from good quality ab initio data. These surfaces are used by the diffusion Monte Carlo algorithm to solve the vibrational Schrödinger equation for the ground state of the above clusters. In addition, the DMC method is used in a size selective study of the N⁺₂-He_n system. Good agreement is obtained with previous theoretical calculations and with the small amount of experimental data available and it is hoped that the predictions made will aid future studies of these clusters. The combined ab initio-Neural-DMC approach is shown to be an efficient method of studying weakly bound molecules and as such will prove to be a useful step towards understanding the structure and bonding of these systems.

Mon projet de thèse a eu pour objectif la construction d'un dispositif expérimental visant à étudier, à très basse température, un mélange de gaz dégénéré composé de deux espèces fermioniques: 6Li et 40K. Une description détaillée du montage de sa mise en place ainsi qu'une caractérisation du dispositif sont présentées. Nous avons réalisé un piège magnéto-optique à deux espèces avec un très grand nombre d'atomes, et un transport magnétique sur une grande distance. Les premières expériences avec le mélange atomique ont permis la première création de molécules hétéronucléaires excitées 6Li40K* par photoassociation. Nous avons enregistré et assigné des spectres de photoassociation pour les états les plus faiblement liés de sept potentiels moléculaires et nous en avons déduit la forme des potentiels à longues distances. Nos résultats ouvrent la voie vers la formation de molécules bosoniques 6Li40K ultra-froides dans leur état fondamental, caractérisé par un grand moment dipolaire électrique permanent. Sur le plan théorique, nous avons développé une nouvelle méthode pour la manipulation des particules quantiques, qui pourrait être appliquée aux molécules 6Li40K. Cette méthode consiste à piéger les particules dans un potentiel oscillant rapidement et induire un changement instantané de phase du potentiel (un saut de phase). Nous montrons que le mouvement moyen des particules peut ainsi être manipulé de manière contrôlée. La méthode proposée a trouvé une première application pour les condensats de Bose-Einstein piégés à l'aide d'un piège magnétique du type "TOP".

High resolution microwave spectra for the transition metal compounds cobalt tri-carbonyl nitrosyl (Co(CO)₃NO), cyclopentadienyl cobalt di-carbonyl (CpCo(CO)₂), and cyclopentadienyl manganese tri-carbonyl (CpMn(CO)₃) were obtained for the first time using pulsed beam Fourier transform spectroscopy. An oblate symmetric top spectrum was measured for Co(CO)₃NO and the first gas phase value of the cobalt nuclear quadrupole coupling parameter was obtained. The asymmetric top hindered rotor spectrum for CpCo(CO)₂ was measured and a barrier to internal rotation was estimated from the spectrum. Analysis of the prolate symmetric top hyperfine spectrum of CpMn(CO)₃ yielded the first gas phase measurement of the rotational constant and the Mn nuclear quadrupole coupling. High resolution microwave spectra for the iron containing transition metal complexes cyclobutadiene iron tri-carbonyl (CbFe(CO)₃), cyclohexadiene iron tri-carbonyl (C-hexFe(CO)₃) were obtained and a Kraitchman analysis of the isotopic substitution data for the butadiene iron tri-carbonyl (BuFe(CO)₃) is also discussed. Structural parameters for the HCCH-CO were obtained from the various isotopomers for this complex. An analysis of the distortion parameter D(J) yielded an estimation of the binding energy for this weakly bound complex. Analysis of spectra for nitrosyl chloride (NOCl) and chlorine tri-fluoride (ClF₃) yielded the first high resolution low J data sets for these molecules. The quadrupole coupling data are interpreted using the Townes-Dailey model for quadrupole coupling and an improved ground state structure for ClF₃ was obtained. Microwave spectra reported here were obtained using a pulsed beam Fourier transform microwave spectrometer constructed at the University of Arizona. The design is similar to original Flygare-Balle apparatus with many modifications for improving signal sensitivity and data acquisition.

It is an aim of this work to provide insight into the energetic influence on the ordering of molecular thin films on crystalline substrates. Here, the term substrate either refers to inorganic crystal surfaces or highly ordered layers of another organic molecular species. In order to calculate the total interface potential of extended molecular domains, a new calculation technique (GRID technique) is developed in the first part of this work. Compared to the standard approach, this method accelerates the potential calculation drastically (times 10000). The other parts of the thesis are dedicated to the comparison of experimental results (obtained by scanning tunneling microscopy and electron diffraction) to the optimal layer structure as predicted by optimization calculations. Potential calculations which are performed for the system perylenetetracarboxylicdianhydride (PTCDA) on graphite demonstrate that point-on-line coincident structures correspond to energetically favorable alignments of the molecular lattice with respect to the substrate lattice. The capability of the GRID technique to predict the optimal layer structure is demonstrated for the system peri-hexabenzocoronene (HBC) on graphite. The organic-organic heteroepitaxy system PTCDA on HBC on graphite is investigated in order to clarify to which extent the ordering mechanism there differs from that of the organic-inorganic heteroepitaxy system PTCDA on graphite. As a result of this investigation, a new type of epitaxy, i.e., substrate induced ordering is found. This new epitaxy type is governed by the inner structure of the substrate lattice unit cell. Here, the substrate surface is a layer of organic molecules itself, hence the substrate surface unit cell does indeed exhibit a complex inner structure. A generalized classification scheme for epitaxial growth incorporating this new type of epitaxy is proposed. In the last chapter, the structure of the first layers of titanylphthalocyanine (TiOPc) on Au(111) is investigated and compared to potential optimization calculations. The correspondence of experimental and theoretical results provides evidence that the GRID technique can, in principle, also be applied to molecular layers on metal surfaces
Das Ziel der vorliegenden Arbeit ist es, Einblicke in die energetischen Einflüsse, die zur Ausbildung der Schichtstruktur organischer Moleküle auf kristallinen Substraten führen, zu geben. Diese Substrate sind entweder Oberflächen anorganische Kristalle oder selbst hochgeordnete Molekülschichten. Um das totale Grenzflächenpotential ausgedehnter Moleküldomänen berechnen zu können, wird im ersten Teil der Arbeit eine neue Berechnungsmethode (GRID Technik) vorgestellt. Im Vergleich mit herkömmlichen Berechnungsmethoden auf der Basis molekülmechanischer Kraftfelder ist diese neue Methode daher um ein Vielfaches schneller (Faktor 100000). Die folgenden Teile der Arbeit sind dem Vergleich experimenteller Ergebnisse (Rastertunnelmikroskopie und Elektronenbeugung) mit, durch Potentialoptimierungsrechnungen als energetisch günstig vorhergesagten, Schichtstrukturen gewidmet. So kann für das System Perylentetracarbonsäuredianhydrid (PTCDA) auf Graphit mittels Potentialberechnungen nachgewiesen werden, daß die experimentell gefundenen ?Point-on-line koinzidenten? Strukturen energetisch günstige Anordnungen des Molekülgitters bezüglich des Substratgitters darstellen. Die Eignung der neuen Berechnungsmethode zur Vorhersage der günstigsten Adsorbatgitterstruktur für ein gegebenes System aus Molekül und Substrat, wird anhand des Systems peri-Hexabenzocoronen (HBC) auf Graphit demonstriert. Das organisch-organische Heteroepitaxiesystem PTCDA auf HBC auf Graphit wird untersucht, um zu klären, inwieweit sich die dafür gültigen Ordnungsmechanismen von denen unterscheiden, die für das Wachstum des organisch-anorganischen Heteroepitaxiesystems PTCDA auf Graphit verantwortlich sind. Dabei gelingt es, eine bisher nicht klassifizierte Art von Epitaxie, d.h. substratinduzierter Ordnung, nachzuweisen. Dieser neue Epitaxietyp ist bedingt durch die innere Struktur einer Substrateinheitszelle - das Substrat ist ja hier selbst eine Schicht geordneter Moleküle, die natürlich eine innere Struktur aufweisen. Im folgenden wird ein verallgemeinertes Klassifizierungssystem für Epitaxietypen abgeleitet, welches den neuen Epitaxietyp beinhaltet. Im letzten Kapitel wird die Struktur von der ersten Lagen von Titanylphthalocyanin (TiOPc) auf Au(111) experimentell untersucht und mit entsprechenden Potentialoptimierungsrechnungen verglichen. Die Übereinstimmung von experimentellen und theoretischen Ergebnissen zeigt, daß die GRID Technik, zumindest prinzipiell, auch für Molekülschichten auf Metallsubstraten anwendbar ist

Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains xv, 99 p.; also includes graphics (some col.). Includes bibliographical references (p. 95-99). Available online via OhioLINK's ETD Center

My research interests during my doctoral years have been focused on high resolution rotational studies of molecules and weakly bound molecular complexes. Information on the molecular structure, internal motions and intermolecular interactions that can be obtained by applying suitable theoretical models to the analysis of these unusually complex spectra allows the determination and understanding of the driving forces involved in formation of the molecular complex. In this way, many types of non-covalent interactions have been characterized, from pure van der Waals interactions in complexes of rare gases to moderate-strength and weak hydrogen bonds (HBs) and to the most recent halogen bonds, pnicogen4 or chalcogen bonds. In this thesis, we first introduce the theory of rotational spectroscopy, including that of the asymmetrical rotor, the effects of centrifugal distortion, nuclear quadrupole coupling effects end those of internal motions In the second part, we introduce the experimental apparatuses that were used and related theoretical knowledge. In the third part, chloropentafluorobenzene (C6F5Cl) and bromopentafluorobenzene (C6F5Br) are chosen as case studies to investigate the effect of perfluorination on the molecular structure and electronic properties.In the fourth and fifth parts, we discuss the 1:1 complexes of acrolein-methanol and acrolein-ethanol. In chapter six to eight I report the results on the microwave detection and analysis of the 1:1 complexes of dimethyl sulfoxide (DMSO) with water, methanol and ethanol, respectively, in the gas phase.

Les gels de protéine nanocomposites sont un sujet encore peu développé dans la littérature malgré de nombreuses applications allant de l’immobilisation d’enzyme aux prothèses en passant par les gels alimentaires. La protéine permet d’assurer la biocompatibilité des gels tandis que l’ajout des nanoparticules a pour but de moduler les propriétés mécaniques des gels. Nous avons donc décidé de nous intéresser aux gels d’hémoglobine réticulée chimiquement et dopés aux nanoparticules. L’hémoglobine (Hb) a été choisie pour sa grande abondance et ses propriétés de fixation du dioxygène. Les gels seront obtenus par réticulation par le glutaraldéhyde (GTA), un dialdéhyde très réactif. Les gels seront dopés par des nanoparticules de silice (NP) afin de comprendre déjà l’effet sur le gel du dopage par des nanoparticules modèles. La première partie de la thèse portera sur l’adsorption de l’hémoglobine sur les nanoparticules de silice afin de lever les dernières inconnues sur ce phénomène déjà étudié. Il sera mesuré les isothermes d’adsorption ainsi que l’activité de l’hémoglobine adsorbée. Les structures de l’hème, de la globine et de l’assemblage Hb/NP seront étudiées avec détails. Par la suite, les études se porteront sur les gels sans et avec nanoparticules afin d’élucider les effets de la gélification et du dopage respectivement. On déterminera les concentrations en Hb, GTA et NP permettant d’obtenir un gel. Puis, comme pour les assemblages Hb/NP, nous nous intéresserons à l’activité et à la structure de Hb (hème et globine). La structuration du gel sera de plus étudiée. Des études sur les propriétés élastiques des gels seront aussi menées et nous finirons sur la dynamique de la protéine gélifiée. Quand il sera possible, l’effet des concentrations des différents composants sera déterminé. Pour toutes ces études, il a été utilisé un vaste panel de techniques de caractérisation classique des protéines ou des gels. Beaucoup d’expériences ont été effectuées sur grands instruments (diffusion de rayonnement, spectroscopie d’adsorption X, dichroïsme circulaire). Des techniques plus accessibles comme la résonance paramagnétique électronique, la rhéologie ou la microscopie électronique ont aussi été employées. Les aspects les plus novateurs de cette thèse ont été l’effet de l’adsorption sur l’hème et la compréhension de la structure de la protéine gélifiée, deux aspects qui n’avaient pas été traités
Nanocomposite protein gels are still an underdeveloped subject in the literature despite many applications ranging from enzyme immobilization to prostheses to food gels. The protein ensures the gel biocompatibility while the addition of the nanoparticles will modulate the gel mechanical properties. We decided to focus on chemically cross-linked hemoglobin gels doped with nanoparticles. Hemoglobin (Hb) was chosen for its high abundance and its oxygen binding properties. The gels will be obtained by crosslinking with glutaraldehyde (GTA), a very reactive dialdehyde. The gels will be doped with silica nanoparticles (NP) in order to understand the effect of doping with model nanoparticles on the gel. The first part of the work will focus on the hemoglobin adsorption on silica nanoparticles in order to resolve the remaining unknowns on this phenomenon, which has already been studied. The adsorption isotherms as well as the activity of the adsorbed hemoglobin will be measured. The structures of the heme, globin and the Hb/NP assembly will be studied in details. Subsequently, works will focus on gels without and with nanoparticles in order to respectively elucidate the effects of gelation and doping. We will determine the concentrations of Hb, GTA and NP to obtain a gel. Then, as with the Hb/NP assemblies, we will look at the activity and structure of Hb (heme and globin).The structuring of the gel will also be studied. Works on the gel elastic properties will also be carried out and we will finish on the dynamics of the gelled protein. When possible, the concentration effect for the different components will be determined. For all these studies, a large panel of conventional technics to characterize proteins or gels was used. Many experiments have been performed in synchrotrons and neutron research centers (radiation scattering, X-ray absorption spectroscopy, circular dichroism). Electronic paramagnetic resonance, rheology or electron microscopy, which are more accessible technics have also been employed. The most innovative aspects of this work were the effect of adsorption on heme and the understanding of the gelled protein structure, two aspects that had not been addressed until now

Ce travail de thèse est consacré à l’étude d’auto-assemblages de molécules organiques π-conjuguées par microscopie à effet tunnel (STM)sous ultra-vide sur une surface de silicium dopée bore. Le manuscrit est constitué de cinq chapitres : dans le premier chapitre, nous présentons un état de l’art des assemblages organiques sur les surfaces métalliques et sur les semi-conducteurs. Le chapitre deux décrit le dispositif expérimental utilisé au cours de cette thèse. Il présente également le substrat de Si(111)-B et fournit les concepts théoriques associés à la microscopie à effet tunnel. Le troisième chapitre décrit en détail les réseaux supramoléculaires obtenus à partir d’une molécule aromatique halogénée de symétrieC2. L’adsorption de 4,4"-dibromo-p-terphényle conduit à la formation de deux types de structures compactes (l’une en bande et l’autre en chevron) stables à température ambiante et commensurables avec la surface. Nous montrons que ces architectures sont pilotées conjointement par la liaison hydrogène, la liaison halogène et du π -stacking. Le quatrième chapitre étudie l’influence du nombre de cycles aromatiques sur la géométrie et la périodicité d’auto-assemblages obtenus sur Si (111) -B. Pour cela, nous avons synthétisé deux molécules organiques composées d’une partie centrale aromatique et de deux chaînes latérales (O-(CH2)9-CH3). La partie centrale est constituée respectivement de trois ou cinq cycles phényles terminées par des groupements cyano. Nous nous sommes également intéressés à l’influence des groupements terminaux sur l’organisation du réseau. Nous montrons que l’effet des groupements cyano sur les interactions "molécule/molécule" et sur les interactions "molécule/surface" est négligeable. A partir des travaux obtenus dans le chapitre 4, nous concluons notre manuscrit en présentant des réseaux supramoléculaires de molécules dipolaires. Ces réseaux forment des lignes de dipôles. Nous montrons que sur de petites échelles les molécules favorisent un alignement de leurs moments dipolaires
This work is dedicated to the investigation under ultra high vacuum of _-conjugated molecule on a silicon surface by means of scanningtunneling microscopy (STM). The manuscript consists of five chapters.In the first chapter, we present a state-of-the-art of organic assembly on metal and semiconductor.Chapter two describes the experimental setup using during thesis. It also shows Si(111)-B substrate and gives theoretical conceptsassociated with the scanning tunneling microscopy.The third chapter describes in detail the supramolecular network obtained from an aromatic halogenated molecule with C2 symmetry. Theadsorption of 4,4"-dibromo-p-terphenyl leads to the formation of two kinds of compacts structures (a stripe structure and a herringbonestructure). The formed networks are stable at room temperature and commensurable with the surface. These architectures are promotedby hydrogen bond, halogen bond and _-stacking.Chapter four studies influence of benzene ring number on the geometry and the periodicity of self-assemblies on Si(111)-B. To do that,we have synthesis two organics molecules composed of an aromatic central part and two laterals chains (O-(CH2)9-CH3). The centralpart is composed of respectively three or five phenyl ring ended by cyano groups. We are also interested to the terminal groups effecton the network organisation. We show that the cyano groups effect on the "molecule/molecule" interaction and the "molecule/surface"interaction are negligible. Basis of the work conducted on the chapter four, we conclude our manuscript by presenting supramolecularsnetworks of dipolar molecule. These networks form dipole lines. We show that on small scale the molecules promote an alignment of theirdipolar moments

The weakly bound association products of atmospherically relevant radical species (O₂, OH, NO₂, HO₂ and NO) have been studied theoretically using quantum-chemical methods. The thermodynamic stabilities, which are crucial to determining the probability of formation in Earth's atmosphere, were calculated for the hydrotrioxy radical (HOOO) and peroxynitrous acid (HOONO, an isomer of nitric acid) relative to the radical dissociation products. In the case of HOONO, the experimentally determined values were confirmed. For HOOO, the predicted stability was significantly lower than the experimentally determined value; a conclusion that was supported by later experimental work and indicates that HOOO will not form in significant quantities in Earth's atmosphere. The fundamental and multi-quantum vibrational transitions were also predicted for both the HOONO and HOOO systems. The theoretical work on the HOONO system aided the assignment of experimental spectra and was used to correct equilibrium rotational constants. The HOOO system presented a challenge for the methods used here and work to apply other approaches in describing the vibrational modes is ongoing. Second-order vibrational perturbation theory, combined with a correlated quantum-chemical method and a moderately sized basis set, provides a method for accurately predicting fundamental and low-order multi-quantum transition energies and intensities for many systems (HOOO being an exception). Here coupled cluster theory, at a level which treats one- and two-electron correlation with a correction for three-electron correlation, and atomic natural orbitals basis sets were used in the vibrational calculations. To predict the dissociation energies of weakly bound species with the precision required (due to the small energy differences involved), high-order correlation contributions (a full treatment of three-electron correlation and a correction for four-electron correlation) are included, as is extrapolation to the basis set limit. Other contributions, such as that for the zero-point energy, were also considered. For the HOOO system, one-dimensional potential curves along the dissociation and torsional coordinates were constructed with standard single-reference and equation-of-motion coupled-cluster methods. The latter is better able to describe the nature of a system in the bond-breaking region and the complex electronic structure of a species formed from two radical fragments, one doubly degenerate in the ground state: X²[Pi] OH and X³[Sigma] O₂. A possible barrier to dissociation and the torsional potential for HOOO were investigated.
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Weak intermolecular interactions have very strong impact on the structures and properties of life giving molecules like H2O, DNA, RNA etc. These interactions are responsible for many biological phenomena. The directional preference of some of these interactions is used for designing different synthetic approaches in the supramolecular chemistry. The work reported in this Thesis comprises of investigations of weak intermolecular interactions in gas phase using home-built Pulsed Nozzle Fourier Transform Microwave (PN-FTMW) spectrometer as an experimental tool and ab-initio and Atoms in Molecules (AIM) theory as theoretical tools. The spectrometer which is coupled with a pulsed nozzle is used to record pure rotational spectra of the molecular clusters in a jet cooled molecular beam. In the molecular beam molecules/complexes are free from interactions with other molecules/complexes and thus, spectroscopy in the molecular beams provides information about the 'isolated' molecule/complex under investigation. The rotational spectra of the molecules/complexes in the molecular beam provide their geometry in the ground vibrational states. These experimental geometries can be used to test the performance and accuracy of theoretical models like ab-initio theory, when applied to the weakly bound complexes. Further the AIM theory can be used to gain insights into the nature and strength of the intermolecular interactions present in the system under investigation. Chapter I of this Thesis gives a brief introduction of intermolecular interactions. Other than hydrogen bonding, which is considered as the most important intermolecular interaction, many other intermolecular interactions involving different atoms have been observed in past few decades. The chapter summarizes all these interactions. The chapter also gives a brief introduction to the experimental and theoretical methods used to probe these interactions. In Chapter II, the experimental and theoretical methods used in this work are summarized. Details of our home-built PN-FTMW spectrometer are given in this chapter. The chapter also discusses briefly the theoretical methods like ab-initio, AIM and Natural bond orbital (NBO) analysis. We have made few changes in the mode of control of one of our delay generators which have also been described. Chapter III and Chapter V of this Thesis are dedicated to the propargyl alcohol complexes. Propargyl alcohol (PA) is a molecule of astrophysical interest. It is also important in combustion chemistry since propargyl radical is considered as the precursor in soot formation. Moreover, PA is a multifunctional molecule, having a hydroxyl (-OH) and an acetylenic (-C≡C-H) group. Both of the groups can individually act as hydrogen bond acceptor as well as donor and thus PA provides an exciting possibility of studying many different types of weak interactions. Due to internal motion of -OH group, PA monomer can exist in gauche as well as trans form. However, rotational spectra of PA-monomer show the presence of only gauche conformer. In Chapter III, rotational spectra of Ar•••PA complex are discussed. The pure rotational spectra of the parent Ar•••PA complex and its two deuterated isotopologues, Ar•••PA-D (OD species) and Ar•••PA-D (CD species), could be observed and fitted within experimental uncertainty. The structural fitting confirmed a structure in which PA is present as gauche conformer and argon interacts with both the O-H group and the acetylenic group leading to Ar•••H-O and Ar•••π interactions respectively. Presence of these interactions was further confirmed by AIM theoretical analysis. In all the three isotopologues c-type rotational transitions showed significant splitting. Splitting patterns in the three isotopologues suggest that it originates mainly due to the large amplitude motion of the hydroxyl group and the motion is weakly coupled with the carbon chain bending motion. No evidence for the complex with trans conformer of PA was found. Although, we could not observe Ar•••trans-PA complex experimentally, we decided to perform ab-initio and AIM theoretical calculations on this complex as well. AIM calculations suggested the presence of Ar•••H-O and a unique Ar•••C interaction in this complex which was later found to be present in the Ar•••methanol complex as well. This prompted us to explore different possible interactions in methanol, other than the well known O-H•••O hydrogen bonding interactions, and eventually led us to an interesting interaction which we termed as carbon bond. Chapter IV discusses carbon bonding interaction in different complexes. Electrostatic potential (ESP) calculations show that tetrahedral face of methane is electron-rich and thus can act as hydrogen/halogen bond acceptor. This has already been observed in many complexes, e.g. CH4•••H2O/HF/HCl/ClF etc., both experimentally and theoretically. However, substitution of one of the hydrogens of methane with -OH leads to complete reversal of the properties of the CH3 tetrahedral face and this face in methanol is electron-deficient. We found that CH3 face in methanol interacts with electron rich sites of HnY molecules and leads to the formation of complexes stabilized by Y•••C-X interactions. This interaction was also found to be present in the complexes of many different CH3X (X=OH/F/Cl/Br/NO2/NF2 etc.) molecules. AIM, NBO and C-X frequency shift analyses suggest that this interaction could be termed as "carbon bond". The carbon bonding interactions could be important in understanding hydrophobic interactions and thus could play an important role in biological phenomena like protein folding. The carbon bonding interaction could also play a significant role in the stabilization of the transition state in SN2 reactions. In Chapter V of this Thesis rotational spectra of propargyl alcohol dimer are discussed. Rotational spectra of the parent dimer and its three deuterated (O-D) isotopologues (two mono-substituted and one bi-substituted) could be recorded and fitted within experimental uncertainty. The fitted rotational constants are close to one of the ab-initio predicted structure. In the dimer also propargyl alcohol exists in the gauche form. Atoms in molecules analysis suggests that the experimentally observed dimer is bound by O-H•••O, O-H•••π and C-H•••π interactions. Chapter VI of the thesis explores the 'electrophore concept'. To observe the rotational spectra of any species and determine its rotational constant by microwave spectroscopy, the species should have a permanent dipole moment. Can we obtain rotational constants of a species having no dipole moment via microwave spectroscopy? Electrophore concept can be used for this purpose. An electrophore is an atom or molecule which could combine with another molecule having no dipole moment thereby forming a complex with a dipole moment, e.g. Argon atom is an electrophore in Ar•••C6H6 complex. The microwave spectra of Ar•••13CC5H6 and Ar•••C6H5D complexes were recorded and fitted. The A rotational constant of these complexes was found to be equal to the C rotational constant of 13CC5H6 and C6H5D molecules respectively and thus we could determine the C rotational constant of microwave 'inactive' 13CC5H6. This concept could be used to obtain the rotational spectra of parallel displaced benzene-dimer if it exists. We recently showed that the square pyramidal Fe(CO)5 can act as hydrogen bond acceptor. Appendix I summarizes the extension of this work and discusses interactions of trigonal bipyramidal Fe(CO)5 with HF, HCl, HBr and ClF. Our initial attempts on generating a chirped pulse to be used in a new broadband spectrometer are summarized in Appendix II. Preliminary investigations on the propargyl•••water complex are summarized in Appendix III.

Weak intermolecular interactions have very strong impact on the structures and properties of life giving molecules like H2O, DNA, RNA etc. These interactions are responsible for many biological phenomena. The directional preference of some of these interactions is used for designing different synthetic approaches in the supramolecular chemistry. The work reported in this Thesis comprises of investigations of weak intermolecular interactions in gas phase using home-built Pulsed Nozzle Fourier Transform Microwave (PN-FTMW) spectrometer as an experimental tool and ab-initio and Atoms in Molecules (AIM) theory as theoretical tools. The spectrometer which is coupled with a pulsed nozzle is used to record pure rotational spectra of the molecular clusters in a jet cooled molecular beam. In the molecular beam molecules/complexes are free from interactions with other molecules/complexes and thus, spectroscopy in the molecular beams provides information about the 'isolated' molecule/complex under investigation. The rotational spectra of the molecules/complexes in the molecular beam provide their geometry in the ground vibrational states. These experimental geometries can be used to test the performance and accuracy of theoretical models like ab-initio theory, when applied to the weakly bound complexes. Further the AIM theory can be used to gain insights into the nature and strength of the intermolecular interactions present in the system under investigation. Chapter I of this Thesis gives a brief introduction of intermolecular interactions. Other than hydrogen bonding, which is considered as the most important intermolecular interaction, many other intermolecular interactions involving different atoms have been observed in past few decades. The chapter summarizes all these interactions. The chapter also gives a brief introduction to the experimental and theoretical methods used to probe these interactions. In Chapter II, the experimental and theoretical methods used in this work are summarized. Details of our home-built PN-FTMW spectrometer are given in this chapter. The chapter also discusses briefly the theoretical methods like ab-initio, AIM and Natural bond orbital (NBO) analysis. We have made few changes in the mode of control of one of our delay generators which have also been described. Chapter III and Chapter V of this Thesis are dedicated to the propargyl alcohol complexes. Propargyl alcohol (PA) is a molecule of astrophysical interest. It is also important in combustion chemistry since propargyl radical is considered as the precursor in soot formation. Moreover, PA is a multifunctional molecule, having a hydroxyl (-OH) and an acetylenic (-C≡C-H) group. Both of the groups can individually act as hydrogen bond acceptor as well as donor and thus PA provides an exciting possibility of studying many different types of weak interactions. Due to internal motion of -OH group, PA monomer can exist in gauche as well as trans form. However, rotational spectra of PA-monomer show the presence of only gauche conformer. In Chapter III, rotational spectra of Ar•••PA complex are discussed. The pure rotational spectra of the parent Ar•••PA complex and its two deuterated isotopologues, Ar•••PA-D (OD species) and Ar•••PA-D (CD species), could be observed and fitted within experimental uncertainty. The structural fitting confirmed a structure in which PA is present as gauche conformer and argon interacts with both the O-H group and the acetylenic group leading to Ar•••H-O and Ar•••π interactions respectively. Presence of these interactions was further confirmed by AIM theoretical analysis. In all the three isotopologues c-type rotational transitions showed significant splitting. Splitting patterns in the three isotopologues suggest that it originates mainly due to the large amplitude motion of the hydroxyl group and the motion is weakly coupled with the carbon chain bending motion. No evidence for the complex with trans conformer of PA was found. Although, we could not observe Ar•••trans-PA complex experimentally, we decided to perform ab-initio and AIM theoretical calculations on this complex as well. AIM calculations suggested the presence of Ar•••H-O and a unique Ar•••C interaction in this complex which was later found to be present in the Ar•••methanol complex as well. This prompted us to explore different possible interactions in methanol, other than the well known O-H•••O hydrogen bonding interactions, and eventually led us to an interesting interaction which we termed as carbon bond. Chapter IV discusses carbon bonding interaction in different complexes. Electrostatic potential (ESP) calculations show that tetrahedral face of methane is electron-rich and thus can act as hydrogen/halogen bond acceptor. This has already been observed in many complexes, e.g. CH4•••H2O/HF/HCl/ClF etc., both experimentally and theoretically. However, substitution of one of the hydrogens of methane with -OH leads to complete reversal of the properties of the CH3 tetrahedral face and this face in methanol is electron-deficient. We found that CH3 face in methanol interacts with electron rich sites of HnY molecules and leads to the formation of complexes stabilized by Y•••C-X interactions. This interaction was also found to be present in the complexes of many different CH3X (X=OH/F/Cl/Br/NO2/NF2 etc.) molecules. AIM, NBO and C-X frequency shift analyses suggest that this interaction could be termed as "carbon bond". The carbon bonding interactions could be important in understanding hydrophobic interactions and thus could play an important role in biological phenomena like protein folding. The carbon bonding interaction could also play a significant role in the stabilization of the transition state in SN2 reactions. In Chapter V of this Thesis rotational spectra of propargyl alcohol dimer are discussed. Rotational spectra of the parent dimer and its three deuterated (O-D) isotopologues (two mono-substituted and one bi-substituted) could be recorded and fitted within experimental uncertainty. The fitted rotational constants are close to one of the ab-initio predicted structure. In the dimer also propargyl alcohol exists in the gauche form. Atoms in molecules analysis suggests that the experimentally observed dimer is bound by O-H•••O, O-H•••π and C-H•••π interactions. Chapter VI of the thesis explores the 'electrophore concept'. To observe the rotational spectra of any species and determine its rotational constant by microwave spectroscopy, the species should have a permanent dipole moment. Can we obtain rotational constants of a species having no dipole moment via microwave spectroscopy? Electrophore concept can be used for this purpose. An electrophore is an atom or molecule which could combine with another molecule having no dipole moment thereby forming a complex with a dipole moment, e.g. Argon atom is an electrophore in Ar•••C6H6 complex. The microwave spectra of Ar•••13CC5H6 and Ar•••C6H5D complexes were recorded and fitted. The A rotational constant of these complexes was found to be equal to the C rotational constant of 13CC5H6 and C6H5D molecules respectively and thus we could determine the C rotational constant of microwave 'inactive' 13CC5H6. This concept could be used to obtain the rotational spectra of parallel displaced benzene-dimer if it exists. We recently showed that the square pyramidal Fe(CO)5 can act as hydrogen bond acceptor. Appendix I summarizes the extension of this work and discusses interactions of trigonal bipyramidal Fe(CO)5 with HF, HCl, HBr and ClF. Our initial attempts on generating a chirped pulse to be used in a new broadband spectrometer are summarized in Appendix II. Preliminary investigations on the propargyl•••water complex are summarized in Appendix III.

Atoms construct the molecules and molecules construct the material substances (with the exceptions as well, e.g.., metals, where atoms directly construct the material substances). Intermolecular interactions play an important role in most of the branches of sciences, ranging from material sciences to biological sciences. Van der Waals interactions are weak intermolecular interactions while hydrogen bonding varies in strength from weak to strong (1 to 40 kcal/mol). The present work focuses on applying some theoretical methods (ab initio and Atoms in Molecules theory) on these interactions to differentiate them with physically meaningful parameters such as hydrogen bond radii and atoms in molecules theory parameters. 1)Defining and calculating H-bond radii have been done using atoms in molecules theory approach which can explain ruling out the presence or absence of an H-bond in an intermolecular interaction. 2) A blue-shift of 200 cm-1 for a weakly bound complex is unprecedented. Our studies on weakly bound complexes showed the blue-shift of 200 cm-1 for H3C•••CIF and shift has been found to be purely from the mixing of normal modes and not because of an interaction. 3)Methane, a symmetric top molecule can act both as H-bond acceptor and donor. The present work shows that methane is rather a better H-bond acceptor than a donor and all the calculated parameters are in favor of this description. 4) Microwave spectrometer is an ultimate tool (at least at present) for structural characterization of the weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer 13CC5H6•••Ar, which is a symmetric top and gives only “B” rotational constant. Moreover, the A rotational constant of the complex is the same as the rotational constant for 13CC5H6, which has no dipole moment. C2H2 molecule is an astrophysically important molecule as it is present in asymptotic giant branch and T-type stars (Teff<3000K). Due to its various infrared active vibrational modes, C2H2 is one of the most important sources in cool stars. The production of C2H2 infrared spectroscopic data at high temperature is therefore essential to trace back physical characteristics of these objects and to model the radiative transfer in their envelope. The databases such as “HITRAN”, do not have enough data available for stimulating high temperature spectra. Keeping all these objectives in mind, high temperature emission spectrum of acetylene has been recorded around 3µm region of acetylene.

Atoms construct the molecules and molecules construct the material substances (with the exceptions as well, e.g.., metals, where atoms directly construct the material substances). Intermolecular interactions play an important role in most of the branches of sciences, ranging from material sciences to biological sciences. Van der Waals interactions are weak intermolecular interactions while hydrogen bonding varies in strength from weak to strong (1 to 40 kcal/mol). The present work focuses on applying some theoretical methods (ab initio and Atoms in Molecules theory) on these interactions to differentiate them with physically meaningful parameters such as hydrogen bond radii and atoms in molecules theory parameters. 1)Defining and calculating H-bond radii have been done using atoms in molecules theory approach which can explain ruling out the presence or absence of an H-bond in an intermolecular interaction. 2) A blue-shift of 200 cm-1 for a weakly bound complex is unprecedented. Our studies on weakly bound complexes showed the blue-shift of 200 cm-1 for H3C•••CIF and shift has been found to be purely from the mixing of normal modes and not because of an interaction. 3)Methane, a symmetric top molecule can act both as H-bond acceptor and donor. The present work shows that methane is rather a better H-bond acceptor than a donor and all the calculated parameters are in favor of this description. 4) Microwave spectrometer is an ultimate tool (at least at present) for structural characterization of the weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer 13CC5H6•••Ar, which is a symmetric top and gives only “B” rotational constant. Moreover, the A rotational constant of the complex is the same as the rotational constant for 13CC5H6, which has no dipole moment. C2H2 molecule is an astrophysically important molecule as it is present in asymptotic giant branch and T-type stars (Teff<3000K). Due to its various infrared active vibrational modes, C2H2 is one of the most important sources in cool stars. The production of C2H2 infrared spectroscopic data at high temperature is therefore essential to trace back physical characteristics of these objects and to model the radiative transfer in their envelope. The databases such as “HITRAN”, do not have enough data available for stimulating high temperature spectra. Keeping all these objectives in mind, high temperature emission spectrum of acetylene has been recorded around 3µm region of acetylene.

The formation of K+···Cl- heavy-Rydberg ion-pair states through dissociative electron attachment in K(np)/CCl4 collisions is investigated. The product ion-pair states are detected directly by electric field-induced dissociation. A Monte Carlo collision code is used to analyze the results that models both the initial Rydberg electron attachment and the subsequent evolution of the ion pairs. The data and the calculations demonstrate the production of long-lived bound K+···Cl- heavy-Rydberg ion pairs. They also suggest that collinear collisions can generate heavy-Rydberg states of low angular momentum.

Intermolecular interactions appear to be well understood in a broad sense today; at a deeper molecular level, it is still evolving. Spectroscopy in this isolated state proved to be a first step toward understanding the intermolecular interaction at the molecular level. Microwave spectroscopy offers precise structural information on the near-equilibrium geometry of small dimers and trimers in isolation. Computational studies like the Atoms in Molecules (AIM), non-covalent index plots (NCI), and natural bond orbital analysis (NBO) are used to augment rotational spectroscopic investigations. The Ka = 1 transitions of H2S dimer and several isotopomers were observed in a pulsed nozzle Fourier transform microwave spectrometer. These transitions give unequivocal proof that, at ultra-low temperatures, hydrogen sulfide forms S-H⸳⸳⸳S hydrogen-bonded dimer in the same way as water does, even though ice and solid H2S seem substantially different in bulk. Also, using the AIM theory, we have shown that H2S dimer satisfies the necessary and sufficient criterion proposed by Koch and Popelier to be hydrogen-bonded. Although we recently highlight the arbitrariness in relying on some computational tools to characterize a bond. The weakly bound trimer between two hydrogen sulfide molecules and one water molecule, (H2S)2H2O, was identified from its rotational spectrum. The break with axial molecular symmetry allowed us to investigate (H2S)2H2O at a level of structural detail that has not yet been possible for (H2O)3 and (H2S)3 with rotational spectroscopy owing to their zero-dipole moment. Analysis of experimental results reveals that the three monomers are bound in a triangular arrangement through S-H⸳⸳⸳S, O-H⸳⸳⸳S, and S-H⸳⸳⸳O hydrogen bonds with a fair amount of co-operativity. High-resolution spectroscopic data may be used to validate the correctness of a model intermolecular potential energy hyper-surface. In this regard, we have measured the donor-acceptor interchange tunnelling splitting in the ground vibrational state of Ar-(H2O)2. In the previous investigations, the donor-acceptor tunnelling splitting in fully deuterated species, Ar-(D2O)2, was measured to be 106 MHz. However, it could not be measured for the Ar-(H2O)2,as the splitting was expected to be several GHz. With the help of a fourfold periodic potential, we have accurately predicted the fingerprints of donor-acceptor interchange tunnelling transitions and measured the splitting of 4257.41(4) MHz in Ar-(H2O)2. Lastly, we have looked beyond hydrogen bonding and explored other intermolecular bonding across the Periodic Table. The slopes of the binding energy versus electron density at the bond critical point were derived for each main group element. Our results show that intermolecular bonding can be classified into two types: intermolecular bonding (IMB) with a shared shell molecule (IMB-S) and intermolecular bonding (IMB) with a closed shell molecule (IMB-C). The IMB-S includes hydrogen, halogen, chalcogen, pnictogen, tetrel (excluding carbon bonds), and boron bonds (but not triel bonds). IMB-C contains lithium, sodium, beryllium, magnesium, triel (excluding boron bonds) and carbon bonds. The binding energy versus electron density plot of the IMB-S class generally has a low slope, whereas the IMB-C type has a high slope. Carbon bonds are distinct from the other members of the group. Carbon is a hesitant partner in tetrel bonds due to the absence of lower energy d-orbitals. The electron density between the two atoms is extremely low, and the binding energy grows fast with electron density, resulting in a high slope value for the carbon bond. The slopes for the Li, Na, Be, Mg, Ca-bonds were found out to be comparable, whereas the slope for the hydrogen bond remains standout. Several similarities eventually lead us to propose a common name, ‘Alkalene bond,’ for the intermolecular bonding in alkali and alkaline earth metals.

The thesis entitled “High-Resolution Charge Density Studies on Electronic Nature of Weak Interactions and Correlation of Molecular Conformation with Packing in Solid State” consist of five chapters. Chapter 1 is a brief introduction to the methodologies and techniques utilized in modelling electron densities and the topics relevant to the work. The subsequent four chapters are divided into two parts-Part A and Part B. Part A has two chapters that discusses the electronic nature of unexplored weak intermolecular interactionspnicogen bonding in nitrogen atom and hydrophobic interactions between methyl groups in molecular crystals. Part B also contains two chapters that investigates the symbiotic relation of molecular conformation and packing in solid state in two unique cases-hybridized induced polymorphism observed in sulfa drug acetazolamide and unusual asymmetry observed in overcrowded Octachloronaphthalene molecule Part A: Electronic Nature of Weak Interactions Chapter 2 discusses the electron density features of pnicogen bond between nitrogen as an electrophile and chlorine as a nucleophile from experimental and theoretical charge density analyses of 2-amino-5-nitropyridine and chloroacetic acid complex. The charge transfer nature of pnicogen bonding due to overlap between donor lone pair orbitals of Cl atom and antibonding N-C sigma star orbital has been demonstrated from gas phase NBO calculations. Presence of sigma hole on N atom is further confirmed from 3D deformation maps and electrostatic maps. Topological description from AIM analysis and energy estimation based on EML method proves this interaction to be weak in nature and comparable to the strength of carbon bonding, type II F•••F halogen bonding. Detailed Cambridge Structural Database (CSD) analysis reveals that planar N atoms have the maximum propensity to participate as electrophile in pnicogen bonding. Chapter 3 reports the frequent occurrence of methyl•••methyl hydrophobic interactions in the solid-state from CSD study with a detailed analysis of these interactions in a series of cocrystals of biologically active molecules such as caffeine, theophylline and tetramethylpyrazine using experimental X-ray charge density analysis, variable-temperature crystallography and solidstate NMR. The visualization of accurate electron density distribution in the interaction region reveals that they are stabilized by the minimized electrostatic repulsion and maximized dispersion forces. This chapter further proves methyl•••methyl HI as a group•••group interaction with a pronounced torsional vibration for the hydrophobic methyl groups which leads to a significant entropic contribution towards its stability. A characteristic C-13 ssNMR up-field chemical shift was found to be associated with these methyl•••methyl interactions in the crystal state. Part B: Correlation of Molecular Conformation with Packing Chapter 4 discusses a new type of polymorphism called hybridized induced polymorphism in connection with the unusual phenomenon of the formation of kinetic form as against the thermodynamic form on slow cooling of boiling aqueous solution of diuretic drug Acetazolamide. Experimental charge density analysis aided with ab initio calculations have investigated the local electron density at the amino region of both polymorphs. A series of crystallization experiments of AZM in aqueous medium were conducted. The boiling solution was ramped down at different rates of cooling; rapid cooling in liquid nitrogen, ambient cooling to room temperature, controlled cooling at (10°C/hr, 7°C/hr and 5°C/hr) to room temperature. PXRD analysis reveals the kinetic form occurs only when the cooling rate is quite slow (7°C/hr and 5°C/hr). The occurrence of both polymorphs from aqueous solution of AZM under different crystallization conditions is rationalized in terms of hybridization induced polymorphism. Chapter 5 investigates electron density distribution in an overcrowded aromatic molecule, Octachloronaphthalene (OCN) by charge density analysis to unravel several unexplored factors responsible for steric hindrance. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge density studies. A new facet in the fundamental understanding of peri interactions is revealed by NCI (Non-Covalent Interaction) analysis. The potential role of these interactions in deforming the molecular geometry and subsequent effect on aromaticity are substantiated from NICS (Nuclear Independent Chemical Shift) and QTAIM (Quantum Theory of Atoms in Molecules) calculations. The eye-catching dissimilarity in the out-of-plane twisting of OCN renders the molecule in an asymmetric geometry in the crystalline phase as compared to symmetric geometry in the optimized solvated phase. This is uniquely characterised by their molecular electrostatic potential (MESP) respectively and is explained in terms of conflict between two opposing forces- peri interactions and symbiotic intermolecular Cl•••Cl and Cl••• contacts.

Les propriétés des matériaux moléculaires proviennent à la fois de la structure des composantes individuelles et de la façon dont elles s’associent. Ce dernier aspect reste difficile à contrôler, malgré de grandes avancées en science des matériaux. Pour mieux comprendre la relation structure-propriétés, nous avons entrepris une étude systématique de l'hexaphénylbenzène et de ses dérivés, qui offrent une charpente symétrique et rigide. En premier lieu, nous avons attaché six groupements diaminotriazinyles sur l’hexaphénylbenzène afin de produire des réseaux tridimensionnels hautement poreux maintenus par des ponts hydrogène. En modifiant systématiquement le coeur moléculaire, nous avons excisé près du tiers de la molécule-mère, générant des réseaux supramoléculaires dont la porosité s’est élevée graduellement jusqu’à 75%, équivalant ainsi le record pour ce type de matériaux. Ensuite, nous avons étudié le comportement de l’hexakis(4-nitrophényl)benzène. Dans les structures cristallines obtenues, des interactions non-covalentes entre groupements nitro démontrent leur potentiel en chimie supramoléculaire. Le coeur moléculaire ne joue qu’un rôle secondaire dans l’empilement des molécules : seules quelques interactions C-H•••π impliquant le cycle aromatique central de l’hexaphénylbenzène sont évidentes. Cette dernière observation nous a poussés à étudier le comportement à l’état cristallin de l’hexaphénylbenzène et ses dérivés. En scrutant attentivement neuf structures cristallines de ces composés, nous avons décerné la présence récurrente d’interactions C-H•••π impliquant le cycle aromatique central. Cette association caractéristique a été exploitée pour créer des réseaux supramoléculaires maintenus par des interactions C-H•••π sélectives entre un groupement éthynyle et le cycle aromatique central de l’hexaphénylbenzène. Finalement, nous avons joint le côté sombre de l’ingénierie cristalline en utilisant nos connaissances dans le but d’empêcher la formation d’interactions directionnelles. En protégeant le cycle aromatique central de l’hexaphénylbenzène à l’aide de groupements alkyles, les interactions C-H•••π ont été pratiquement éliminées. Ces résultats offrent la possibilité de créer de nouveaux matériaux amorphes. Dans ces études, focalisées sur le système hexaphénylbenzène, nous avons mis en relief des phénomènes qui sont obscurcis dans d'autres familles de molécules. De plus, ce système a grandement facilité l’utilisation d’une approche méthodique pour explorer la relation structure-propriétés. Nos travaux nous ont amenés à des conclusions de valeur universelle en science des matériaux moléculaires.
The properties of molecular materials depend on the identity of individual components and on their organization. Unfortunately, it remains difficult to control molecular organization, despite advances in materials science. To better understand the relationship between molecular structure and collective properties, we undertook a systematic study of hexaphenylbenzene and its derivatives, which possess a rigid symmetric framework. Our first study focused on using hydrogen bonds to control self-assembly in the solid state. By installing six diaminotriazinyl groups on a hexaphenylbenzene core, we predictably obtained highly porous three-dimensional hydrogen-bonded networks. Through systematic structural modifications of the molecular core, we excised nearly a third of the parent molecule, and the porosity of the networks gradually increased, matching the record of 75% previously obtained for this type of material. We then turned to weaker interactions to control organization, as revealed by the packing of hexakis(4-nitrophenyl)benzene. In the crystal structures analyzed, non-covalent interactions between nitro groups were observed, demonstrating their potential in supramolecular chemistry. Careful examination of the structures showed that the hexaphenylbenzene moieties play only a secondary role in determining the overall packing; however, C-H•••π interactions involving the central aromatic ring of hexaphenylbenzene were also observed. To further document this unexpected behavior, we analyzed nine crystal structures of hexaphenylbenzene and derivatives, which showed that a C-H•••π recognition pattern involving the central aromatic ring occurs consistently throughout the series. This motif was used to prepare supramolecular networks based exclusively on selective and directional C-H•••π interactions involving ethynyl groups and the central aromatic ring of hexaphenylbenzene. Finally, we joined the dark side of crystal engineering by using our knowledge of supramolecular chemistry to prevent the formation of directional interactions. By installing alkyl groups near the central aromatic ring of hexaphenylbenzene, C-H•••π interactions were practically eliminated. These results were then used to devise new amorphous materials. The hexaphenylbenzene system permitted a methodical analysis of structure-property relationships in molecular materials. This particular system exposed phenomena normally obscured in other families of molecules, and our analysis of its behavior has yielded conclusions of universal value in materials science.