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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Rotational Specroscopic And Theoretical Investigations Of Non-conventional Hydrogen Bonds

Aiswarya Lakshmi, P 12 1900 (has links) (PDF)
The nature of interactions within a molecule, i.e. chemical bonding, is well understood today. However, our understanding about intermolecular interactions, which has great relevance in nature, is still evolving. Historically there are two types of intermolecular interactions, van der Waals interaction and hydrogen bonding. However, there has been an upsurge of interest in the halogen bonding and lithium bonding during the last decade. The main emphasis of our research is to understand these interactions in detail, in particular non-conventional hydrogen bond acceptors. In this work, weakly bound complexes are studied using Pulsed Nozzle Fourier Transform Microwave Spectrometer, which has been fabricated in our laboratory and various theoretical methods. FTMW spectroscopy in the supersonic beam provides accurate structural information about the near-equilibrium geometry of small dimers and trimers in isolation. The home-built Pulsed Nozzle Microwave spectrometer, having a spectral range of 2-26.5 GHz has been used to record the microwave spectrum of these complexes. The spectrometer consists of a Fabry-Perot cavity, electronic circuit and pumps. Fabry-Perot cavity is the interaction zone of the molecules and radiation. The electronic circuit is used for the polarization and detection of the signal. Mechanical and diffusion pumps are used to maintain the vacuum inside the cavity. The gas molecules of interest are then mixed with a carrier gas and pulsed supersonically inside the cavity through a nozzle of 0.8 mm diameter. The emission from the complexes formed during the expansion is detected by super-heterodyne detection technique and then Fourier transformed. The first chapter of the thesis gives a brief introduction to intermolecular interactions, hydrogen bonding, halogen bonding, lithium bonding and molecular 2 of clusters. The chapter also includes a brief introduction to rotational spectroscopy. The second chapter of the thesis discusses the experimental and theoretical methods. It includes a detailed discussion of the mechanical and electrical parts of the spectrometer and the software used, which is developed in Labview 7.1. The various theoretical methods (ab initio and DFT) and the basis sets are discussed along with Atoms In Molecules Theory and the criteria used to characterize hydrogen bond. In the third chapter, to understand the ability of saturated hydrocarbons to act as hydrogen bond donor and acceptor, interaction of CH4 with H2S is studied using rotational spectroscopy as well as theoretical methods such as ab initio and Atoms In Molecules theory. Three progressions were obtained for the CH4•••H2S complex using microwave spectroscopy. The progressions were independently fitted to a linear top Hamiltonian. Absence of J10 transition in Progression II confirms the presence of higher internal angular momentum state, m=1. This also confirms the internal rotation of the monomers in the complex. Progressions II and III have negative centrifugal distortion constants. Hence both the states are from some excited internal rotation/torsional motion with strong vibrational-rotational coupling. The moment of inertia obtained from the experimental rotational constant confirms the structure in which sulphur of H2S is close to CH4. This also supports the structure in which CH4 is the hydrogen bond donor, if such an interaction is present. AIM analysis and the potential energy barrier for internal rotation show orientational preference and hence hydrogen bonding. The ab initio results show that CH4•••HSH interaction is more favorable than CH3H•••SH2. Ab initio and AIM studies also gave a structure where there is direct interaction between C and S. This is interesting since the electronegativities of C and S are comparable. Experimentally obtained negative distortion constants for the other two states, confirm excited state rotational-vibrational coupling. The experimental data give a floppy structure having internal rotation. In the fourth chapter the complex chosen for investigation is benzene-ethylene. Experiments in condensed phase and theoretical works show evidence of - stacking in benzene dimer, but there is no gas phase spectroscopic evidence available for the same. The lack of permanent dipole moment in the -stacked geometry of benzene dimer is the hindrance in the experimental observation of the same using microwave spectroscopy. Substitution of one of the benzene with ethylene in the -stacked structure will result in a complex having permanent dipole moment. C6H6 C2H4 complex can have, in addition to -stacking, C-H/interaction. There could be a competition between C6H6 and C2H4, either of which can act as H-bond donor. Experiments show the evidence of C-H/interaction, where C2H4 is the hydrogen bond donor. To ascertain hydrogen bond interaction AIM analysis has been carried out. The results show C-H/interaction, where one of the C2H4 hydrogen interacts with the benzene. Even though the aim was to get the -stacked geometry, it could not be obtained. However theory and AIM supports the formation of -stacked complex. In the fifth chapter using theoretical methods the ability of radicals as acceptor of hydrogen, lithium and chlorine bonds are examined with CF3 radical as the model system. As hydrogen bonds are highly sensitive to the environment, the effect of substitution of hydrogen by fluorine is also analyzed. It is found that, even though CH3 and CF3 radicals are topologically different, they interact in a similar fashion. AIM analysis of CF3HY satisfies all the eight criteria proposed by Koch and Popelier for hydrogen bonding. Here the hydrogen bond formed is charge transfer assisted. The interaction energies of the complexes are inversely proportional to the dipole moment of hydrogen bond donors and are proportional to the charge transfer occurring in the complex. Interaction energies from ab initio calculations confirm complexation of CF3 radical with LiY(Y=F, Cl, Br) and ClF. AIM analysis of CF3LiY and CF3ClF complexes show a bond critical point between Li/Cl and the C of CF3 and the condition of mutual penetration is also met. In CF3LiY complexes the interaction energies and charge transferred are directly proportional to the dipole moment of the Li bond donor. In the sixth chapter in order to extend the concept of non-conventional hydrogen bond acceptors to transition metals, complexes of Fe (Fe(CO)5) with HX (X=F,Cl,Br) have been studied theoretically. DFT calculations show that the structure in which the hydrogen of HX interacting with Fe through the sixth co-ordination site is a stable geometry. AIM analysis shows the presence of a bond critical point between the iron and the hydrogen of HX and hence bond formation. Q obtained from NBO analysis shows that there is charge transfer from the organometallic system to the hydrogen bond donor. However the interaction energies of the complexes are proportional to the dipole moment of hydrogen bond donors and are inversely proportional to the charge transfer for these complexes. H-bonding leads to the stabilization of square pyramidal geometry. ‘Hydrogen bond radius’ of iron has also been defined. Studies on the interaction of Fe(CO)5 with ClF and ClH showed that Fe can also act as a chlorine bond acceptor. Seventh chapter provides the overall conclusion and also discusses future direction.
2

Microwave Spectroscopic and Atoms in Molecules Theoretical Investigations on Weakly Bound Complexes : From Hydrogen Bond to 'Carbon Bond'

Devendra Mani, * January 2013 (has links) (PDF)
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.
3

Microwave Spectroscopic and Theoretical Investigations on Inter/Intra Molecular Bonding

Shahi, Abhishek January 2014 (has links) (PDF)
The importance of weak interactions between molecules to life and all parts of science and engineering is unquestionable and there have been an enormous interest in such interactions. Among all the weak interactions, hydrogen bonding is the most popular and it has enjoyed the most attention of the scientific community. Halogen bonding is gaining more popularity in the recent time, as its importance to biological molecules and crystal engineering has been recognized. In this work, a Pulsed Nozzle Fourier Transform Microwave spectrometer has been used to study the rotational spectra of molecules and hydrogen bonded complexes. Structural information is obtained from the rotational spectra. Ab initio electronic structure, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theoretical methods have been used to characterize the weak intermolecular interactions, including hydrogen bonding, halogen bonding and lithium bonding. In Chapter I, introduction to weak interaction is discussed. A brief introduction of different experimental and theoretical methods is presented. Chapter II discusses in detail about the different methods used to investigate weak interaction, both experimentally and theoretically, in this work. In our lab, we use Pulsed Nozzle Fourier Transform Microwave spectrometer to determine the complexes spectra and structures. We generate MW radiation with the help of electronic devices and use Balle-Flygare cavity where molecular interaction takes place. We inject the sample inside the cavity in form of supersonic molecular beam through a pulsed nozzle, parallel to MW radiation. The detailed instrumental discussion about MW spectrometer has been done in this Chapter. We extensively use theoretical methods to probe weak bonding and characterize them. Ab initio and DFT calculations are used to optimize the structure of the complexes and predict their rotational spectra. Atoms in Molecules theory and Natural Bond Orbital theory are then used with the ab initio wave functions to understand the weak interactions in depth. Discussion about these methods and software used for the analysis will also be discussed. In Chapter III, rotational spectrum of Hexafluoroisopropanol (HFIP) monomer is presented. HFIP is an interesting molecule as it offers many possibilities as hydrogen bond donor and acceptor. It has the OH group which can both accept/donate a hydrogen bond and in addition it has a very acidic CH group. It is the only solvent that can dissolve polyethylene terephthalate, a normally difficult-to-dissolve polymer, and clearly it has unique interactions with this difficult to solve polymer. We have recorded and fitted rotational spectra of five different isotopologues of HFIP which helped us in determining its accurate structure. Though, it can exist in synclinical and antiperiplanar conformers, only the later has been detected in our molecular beam spectrometer. This happens to be the global minimum structure of HFIP. Combination of experimental observations and ab initio calculations provided many evidences which confirmed the presence of antiperiplanar conformer, experimentally. Since, the rotational constants for both conformers were very close, it was always challenging to pick up one conformer as experimentally observed structure. A prototype molecule, hexafluoroisobutene (HFIB) shows doubling of rotational transitions due to tunnelling/counter rotation of the two CF3 groups through a small barrier. Interestingly, such motion has no barrier in HFIP and hence no splitting in transitions was observed. Potential energy surface calculated for counter-rotation of the two CF3 groups is consistent with this observation. This barrier is different from eclipsed-staggered exchange barrier, observed by 60 counter rotation of both terminal CF3 groups, for which the barrier height is very large and tunnelling cannot occur. The origin/lack of the small barrier in HFIB/HFIP has been explored using Natural Bond Orbital (NBO) method which helped in understanding intramolecular bonding in these molecules. Along with HFIB, other prototype molecules were also considered for the analysis e.g. hexafluoroacetone, hexafluoroacetone imine, hexafluoroisobutane, hexafluoroisopropylamine. In the last section of this Chapter, we have discussed the generalized behaviour of molecules which have CF3-C-CF3 groups. In Chapter IV, rotational spectrum of HFIP•••H2O complex is presented. Aqueous solution of HFIP stabilizes α-helical structure of protein, a unique property of this solvent. The main objective of this Chapter is understanding the interaction between HFIP and H2O. Microwave spectrum of HFIP•••H2O was predicted and recorded. Three isotopologues were investigated. Though, this complex could in principle have several structural conformers, detailed ab initio calculations predicted two conformers and only one was observed. Though, the rotational constants for both structures were somewhat similar, lack of a dipole transitions, larger intensity of b-dipole transitions over c-dipole transitions and isotopic substitution analysis positively confirm the structure in which HFIP acts as the hydrogen bond donor. The linear O-H•••O hydrogen bond in HFIP-H2O complex is significantly stronger than that in water dimer with the H•••O distance of 1.8 Å. The other structure for this complex, not found in experiment is cyclic with both C-H•••O and O-H•••O hydrogen bonds, both of which are bent with H•••O distances in the range 2.2-2.3 Å. Both AIM and NBO calculations have been used to characterize the hydrogen bond in this complex. In Chapter V, a comprehensive study on hydrogen bonding, chlorine bonding and lithium bonding have been done. A typical hydrogen bonded complex can be represented as A•••H-D, where A is the acceptor unit and H-D is the hydrogen bond donor unit. Many examples are known in literature, both experimentally and theoretically, in which the A-H-D bond angles are not linear. Deviation from linearity also results in the increase in A•••H bond lengths, as noted above for the two structures of HFIP•••H2O complex. Though this has been known for long, the distance between A and D being less than the sum of their van der Waals ‘radii’ is still used as a criterion for hydrogen bonding by many. Our group has recently shown the inappropriateness of van der Waals ‘radii’ and defined hydrogen bond ‘radii’ for various donors, DH and A. A strong correlation of DH hydrogen bond ‘radii’ with the dipole moment was noted. In this Chapter, we explored in detail the angular dependence of hydrogen bond ‘radii’. Electron density topology around DH (D = F, Cl and OH) has been analyzed in detail and shown to be elliptical. For these molecules, the two constants for H atom treated as an ellipse have been determined. It is hoped that these two constants will be used widely in analyzing and interpreting H•••A distances, as a function of D-H•••A angles, rather than one ‘radius’ for H and acceptor atoms. In Chapter VI, Detailed analysis and comparisons among hydrogen bond, chlorine bond and lithium bond, have been done. Hydrogen can be placed in group 1 as well as group 17 of the periodic table. Naturally, lithium bonding and halogen bonding have been proposed and investigated. There have been numerous investigations on the nature of hydrogen bonding and the physical forces contributing to it. In this Chapter, a total of one hundred complexes having H/Cl/Li bonding have been investigated using ab initio, AIM and NBO theoretical methods. Various criteria proposed in the literature have been examined. A new criterion has been proposed for the characterization of closed shell (ionic/electrostatic) and open shell (covalent) interactions. It has been well known that the D-H bond weakens on the D-H•••A hydrogen bond formation and H•••A bond acquires a fractional covalency. This Chapter shows that for D-Li•••A complexes, the ionicity in D-Li is reduced as the Li•••A bond is formed This comprehensive investigation of H/Cl/Li bonding has led us to propose a conservation of bond order, considering both ionic and covalent contributions to both D-X and X•••A bonds, where DX is the X-bond donor and A is the acceptor with X = H/Cl/Li. Hydrogen bond is well understood and its definition has been recently revised [Arunan et al. Pure Appl. Chem., Vol. 83, pp. 1619–1636, 2011]. It states “The X–H•••Y hydrogen bond angle tends toward 180° and should preferably be above 110°”. Using AIM theory and other methods, this fact is examined and presented in Appendix A. In second part of appendix A, a discussion about calling H3¯ complex as trihydrogen bond and its comparison with FHF¯ complex, is presented. In Appendix B, there is tentative prediction and discussion about the HFIP dimer. Condense phase studies show that HFIP have strong aggregation power to form dimer, trimer etc. During, HFIP monomer study, we have unassigned lines which are suspected to be from HFIP dimer. These are tabulated in the Appendix B as well.

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