Quantum Mechanical Studies of Charge Assisted Hydrogen and Halogen Bonds

This dissertation is mainly focused on charge assisted noncovalent interactions specially hydrogen and halogen bonds. Generally, noncovalent interactions are only weak forces of interaction but an introduction of suitable charge on binding units increases the strength of the noncovalent bonds by a several orders of magnitude. These charge assisted noncovalent interactions have wide ranges of applications from crystal engineering to drug design. Not only that, nature accomplishes a number of important tasks using these interactions. Although, a good number of theoretical and experimental studies have already been done in this field, some fundamental properties of charge assisted hydrogen and halogen bonds still lack molecular level understanding and their electronic properties are yet to be explored. Better understanding of the electronic properties of these bonds will have applications on the rational design of drugs, noble functional materials, catalysts and so on. In most of this dissertation, comparative studies have been made between charge and neutral noncovalent interactions by quantum mechanical calculations. The comparisons are primarily focused on energetics and the electronic properties. In most of the cases, comparative studies are also made between hydrogen and halogen bonds which contradict the long time notion that the H-bond is the strongest noncovalent interactions.Besides that, this dissertation also explores the long range behavior and directional properties of various neutral and charge assisted noncovalent bonds

The Magnitude and Mechanism of Charge Enhancement of CH∙∙O H-bonds

Quantum calculations find that neutral methylamines and thioethers form complexes, with N-methylacetamide (NMA) as proton acceptor, with binding energies of 2–5 kcal/mol. This interaction is magnified by a factor of 4–9, bringing the binding energy up to as much as 20 kcal/mol, when a CH3+ group is added to the proton donor. Complexes prefer trifurcated arrangements, wherein three separate methyl groups donate a proton to the O acceptor. Binding energies lessen when the systems are immersed in solvents of increasing polarity, but the ionic complexes retain their favored status even in water. The binding energy is reduced when the methyl groups are replaced by longer alkyl chains. The proton acceptor prefers to associate with those CH groups that are as close as possible to the S/N center of the formal positive charge. A single linear CH··O hydrogen bond (H-bond) is less favorable than is trifurcation with three separate methyl groups. A trifurcated arrangement with three H atoms of the same methyl group is even less favorable. Various means of analysis, including NBO, SAPT, NMR, and electron density shifts, all identify the +CH··O interaction as a true H-bond

Anion–Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment

Ab initio calculations are applied to the question as to whether a AeX5− anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F−, Cl−, or CN−. The latter approaches the central Ae atom from above the molecular plane, along its C5 axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier

The Halogen Bond

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

Effects of Charge and Substituent on the S∙∙∙N Chalcogen Bond

Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of 37 kcal/mol for X = F. The binding is weakened to some degree when the H atoms are replaced by methyl groups in XMe2S+···NH3. The source of the interaction in the charged systems, like their neutral counterparts, is derived from a charge transfer from the N lone pair into the σ*(SX) antibonding orbital, supplemented by a strong electrostatic and smaller dispersion component. The binding is also derived from small contributions from a CH···N H-bond involving the methyl groups, which is most notable in the weaker complexes

Pseudohalide tectons within the coordination sphere of the uranyl ion: experimental and theoretical study of C-H···O, C-H···S, and chalcogenide noncovalent interactions

A series of uranyl thiocyanate and selenocyanate of the type [R4N]3[UO2(NCS)5] (R4 = nBu4, Me3Bz, Et3Bz), [Ph4P][UO2(NCS)3(NO3)] and [R4N]3[UO2(NCSe)5] (R4 = Me4, nPr4, Et3Bz) have been prepared and structurally characterized. The resulting noncovalent interactions have been examined and compared to other examples in the literature. The nature of these interactions is determined by the cation so that when the alkyl groups are small, chalcogenide···chalcogenide interactions are present, but this “switches off” when R = nPr and charge assisted U═O···H–C and S(e)···H–C hydrogen bonding remain the dominant interaction. Increasing the size of the chain to nBu results in only S···H–C interactions. The spectroscopic implications of these chalcogenide interactions have been explored in the vibrational and photophysical properties of the series [R4N]3[UO2(NCS)5] (R4 = Me4, Et4, nPr4, nBu4, Me3Bz, Et3Bz), [R4N]3[UO2(NCSe)5] (R4 = Me4, nPr4, Et3Bz) and [Et4N]4[UO2(NCSe)5][NCSe]. The data suggest that U═O···H–C interactions are weak and do not perturb the uranyl moiety. While the chalcogenide interactions do not influence the photophysical properties, a coupling of the U═O and δ(NCS) or δ(NCSe) vibrational modes is observed in the 77 K solid state emission spectra. A theoretical examination of representative examples of Se···Se, C–H···Se, and C–H···O═U by molecular electrostatic potentials and NBO and AIM methodologies gives a deeper understanding of these weak interactions. C–H···Se are individually weak but C–H···O═U interactions are even weaker, supporting the idea that the -yl oxo’s are weak Lewis bases. An Atoms in Molecules study suggests that the chalcogenide interaction is similar to lone pair···π or fluorine···fluorine interactions. An oxidation of the NCS ligands to form [(UO2)(SO4)2(H2O)4]·3H2O was also noted

“Co-crystallisation of active pharmaceutical ingredients”

In the thesis presented here, novel co-crystals of two active pharmaceutical ingredients (APIs), i.e. paracetamol and furosemide are presented. Co-crystals are molecular complexes in which two or more components are held together through non-covalent interactions. The work on co-crystals was aimed to investigate and identify robust hydrogen bonds and primary structural motifs which can be used to predict the solid-state assembly in related molecular complexes. The Database mining based on retro-synthetic approach followed by co-crystal screening using mechano-chemical and crystallisation methods in conjunction with high-throughput powder X-ray analysis led to the discovery of four novel co-crystal forms of paracetamol. The study shows that a balance between the retrosynthetic approach and database screening of supramolecular synthons provides a useful approach for targeted co-crystal synthesis. The ability of charge transfer hydrogen bonding interaction to drive the assembly of molecules in co-crystals was investigated. This led to the synthesis of a series of isostructural host-guest complexes of furosemide. It has been discovered that charge transfer interaction drives the crystal packing arrangement in presence of other hydrogen bonding interactions. The ability of two component physical mixture to form ternary co-crystals has been investigated. Systematic synthesis with careful selection of components based on simple geometric principles led to the discovery of a series of ternary co-crystals stabilised through a novel two-dimensional hydrogen-bonded network, which serves a prototype for a new family of ternary co-crystals. This has enabled a targeted approach for the selection and synthesis of new ternary co-crystals with control over symmetry and gross structural features. The study demonstrates that networks that maintain their dimensionality and integrity provide a degree of predictability in the crystal packing arrangements in the solid state

Coordination of phosphido-boratabenzene ligands to transition metals

Environ 90% des composés produits industriellement sont fabriqués à l'aide de catalyseurs. C'est pourquoi la conception de catalyseurs toujours plus performants pour améliorer les procédés industriels actuels est toujours d’intérêt. De la grande variété de complexes avec des métaux de transition rapportés jusqu'à présent, les complexes zwitterioniques attirent notre attention par leurs activités catalytiques souvent supérieures aux complexes cationiques normaux. Un complexe métallique zwitterionique est un fragment métal-ligand neutre où la charge positive est située sur le centre métallique et où la charge négative est délocalisée sur un des ligands liés au métal. Nous proposons la synthèse de ligands anioniques phosphine comportant des groupements borates et boratabenzènes. Cette dernière espèce est un cycle à 6 membres où l’un des atomes de carbone est remplacé par un atome de bore et qui est négativement chargé. La capacité de ces phosphines anioniques à se lier à un centre métallique à l’aide de la paire libre du phosphore est due à la nature du lien P-B qui défavorise l’interaction entre la paire libre du phosphore et l’orbitale p vide du bore. Les propriétés de di-tert-butylphosphido-boratabenzène (DTBB) comme ligand phosphine anionique hautement donneur et encombré ainsi que la découverte de ses modes de coordination inhabituels pour stabiliser les métaux de transition insaturés ont été étudiés au cours de ce travail. De nouvelles perspectives sur les modes de coordination de phosphido-boratabenzène et la force de l’interaction du lien P-B seront discutées ainsi que les applications catalytiques. Nous avons d’abord étudié la coordination η1 avec des complexes de fer, ce qui nous a fourni des données quantitatives précieuses sur la capacité du DTBB d’agir comme ligand très donneur par rapport aux autres ligands donneurs bien connus. La capacité du DTBB à changer de mode de coordination pour soutenir les besoins électroniques du métal a été démontrée par la découverte d’une nouvelle espèce ferrocenyl phosphido-boratabenzène et sa nucléophilie a été étudiée. Au meilleur de notre connaissance, aucun exemple d’un ligand boratabenzène coordonné aux métaux du groupe 11 n’existe dans la littérature. Voilà pourquoi nous avons décidé d’explorer les modes de coordination du ligand DTBB avec Cu(I), Ag(I) et Au(I). A notre grande surprise, le ligand DTBB est capable de stabiliser les métaux du groupe 11 aux états d’oxydation faibles par une liaison MP qui est une coordination du type η1, un mode de coordination guère observé pour les ligands boratabenzène. Pendant nos travaux, notre attention s’est tournée vers la synthèse d’un complexe de rhodium(I) afin de tester son utilité en catalyse. A notre grande satisfaction, le complexe Rh-DTBB agit comme un précatalyseur pour l’hydrogénation des alcènes et alcynes à la température ambiante et à pression atmosphérique et son activité est comparable à celle du catalyseur de Wilkinson. Dans un désir d’élargir les applications de notre recherche, notre attention se tourna vers l’utilisation des composés du bore autres que le boratabenzène. Nous avons décidé de synthétiser une nouvelle espèce phosphido-borate encombrée. Lorsqu’elle réagit avec des métaux, l’espèce phosphido-borate subit un clivage de la liaison P-B. Toutefois, cette observation met en évidence la singularité et les avantages de la stabilité de la liaison P-B lors de l’utilisation du fragment boratabenzène. Ces observations enrichissent notre compréhension des conditions dans lesquelles la liaison P-B du ligand DTBB peut être clivée. Ces travaux ont mené à la découverte d’un nouveau ligand ansa-boratabenzène avec une chimie de coordination prometteuse.About 90% of industrially produced compounds are made using catalysts. This is why the design of ever more efficient catalysts to improve the current industrial processes remains a subject of interest. A wide variety of complexes with transition metals have been reported so far. Amongst the plethora of metal complexes used as catalysts, zwitterionic complexes are of particular interest due to their increased catalytic activity that often surpasses that of their cationic parent complexes. A zwitterionic complex is a neutral metal-ligand fragment where the positive charge is localized over the metal center and the negative charge is delocalized over the ligands. In order to generate new zwitterionic complexes, we are looking at the coordination chemistry of anionic phosphine ligands bearing boratabenzene functionalities. Boratabenzene is a six-membered heterocycle where one of the C-H fragments has been replaced by a negatively charged B-X fragment. The ability of these anionic phosphines to bind to a metal center by the phosphorous lone pair is due to the nature of the P-B interaction, which disfavours orbital overlap between the lone pair of electrons on phosphorous and the empty p orbital on boron. The properties of di-tert-butylphosphido-boratabenzene (DTBB) as a highly donating and bulky anionic phosphine ligand and the discovery of its unusual coordination modes to stabilize unsaturated transition metals has been explored in the course of this work. New insights into the coordination modes of phosphidoboratabenzene and on the strength of the P-B interaction will be discussed. Catalytic applications of the synthesized complexes will also be presented. First we studied the η1 coordination of DTBB to iron, which had provided valuable quantitative data about the donating capability of the aforementioned ligand against other well-known good donors. The DTBB’s capability to change coordination modes in order to support the electronic needs of the metal has been demonstrated by the discovery of a new pendant ferrocenyl-like phosphidoboratabenzene species and its nucleophilicity has been proved. To the best of our knowledge, no example of a boratabenzene ligand coordinated to group 11 metals has been reported in the literature. This is why we decided to explore the coordination modes of DTBB ligand with Cu(I), Ag(I) and Au(I). To our surprise, the DTBB ligand is capable to stabilize group 11 metals in a low oxidation state featuring a M-P bond by means of a η1 coordination, a scarcely observed coordination mode for boratabenzene ligands. Looking for applications of boratabenzene complexes in catalysis, our attention turned to the synthesis of a rhodium(I) complex. To our delight, the DTBB–Rh complex acts as a precatalyst for the hydrogenation of alkenes and alkynes at room temperature and atmospheric pressure and its activity is comparable to that of Wilkinson’s catalyst. Finally in a desire to expand the concepts of our research, our attention turned to explore the use of alternatives to the boratabenzene moiety. We decided to synthesize a new bulky phosphido-borate species. When reacted with metals, the phosphido-borate undergoes a cleavage of the P-B bond. However, this finding sets forward the singularity and advantage of the P-B bond in boratabenzene moieties. This observations also enrich our understanding of the conditions under which the P-B bond on DTBB ligand can be cleaved; evidence that lead to the discovery of a new ansa-boratabenzene ligand with promising coordination chemistry

Proton transfer, electron binding and electronegativity in ammonium-containing systems

Using modern electronic structure methods, the ammonia-hydrogen halide complexes and their anions are characterised to determine the number, type, and properties of their minima, and their electron binding energies. Methodological issues of determining the potential energy surfaces of reactive monomers are addressed in the course of this investigation. The energetic origins of the hydrogen-bonded minima are determined by evaluation of the one-body and two-body terms composing the total energy of the complexes, and a rationale for the drive to proton transfer is presented. It is concluded that the systems have qualitatively similar potential surfaces, and that the balance of the one-body and two-body forces determines the number and depth of minima, while the electron acts as a perturbing agent on the one- or two-body energy, depending upon the nature of the minimum encountered. The halogen-bonded structures of ammonia-hydrogen bromide, iodide, and astatide complexes are shown to be stable, and one may perhaps bind an electron. The concept of the ammonium radical as a pseudo-atom is presented and tested. It is found to show competing pseudo-atomic and molecular properties.Engineering and Physical Sciences Research Council (EPSRC