Academic literature on the topic 'Hydrogen Bond Dimer'

Two forms of cyclic, doubly hydrogen-bonded dimers are discovered for crystalline 1H-pyrrolo[3,2-h]quinoline, a bifunctional molecule possessing both hydrogen bond donor and acceptor groups. One of the forms is planar, the other is twisted. Analysis of IR and Raman spectra, combined with DFT calculations, allows one to assign the observed vibrations and to single out vibrational transitions which can serve as markers of hydrogen bond formation and dimer structure. Raman spectra measured for samples submitted to high pressure indicate a transition from the planar towards the twisted structure. Formation of intermolecular hydrogen bonds leads to a large increase of the Raman intensity of the NH stretching band: it can be readily observed for the dimer, but is absent in the monomer spectrum.

Molecules of the title compound, C8H11NOS, are flat and almost C s-symmetric. Bond lengths and angles resemble calculated values at the B3LYP/6-311+G(2 d,p) level of theory. The solid is characterized by van der Waals bonding and π stacking (stacking distance = 3.352 Å) of the basic motif of the structure: planar centrosymmetric dimers that are bonded by pairs of symmetry-equivalent N—H...S bonds. The dimer structure is rationalized by the nature of the hydrogen-bond acceptor orbital, the S(3p) orbital located in the molecular plane. The double-donor–double-acceptor situation in the dimer results in an unusual C=S...H angle of about 127° which is large compared with isolated C=S...H bonds (circa 100°), but small compared with the almost linear acceptor geometry in related oxo compounds.

The title compound, C14H20N2OS2[systematic name:S-hexyl (E)-2-(2-hydroxybenzylidene)hydrazine-1-carbodithioate], crystallizes with four independent molecules (A–D) in the asymmetric unit. All four molecules adopt anEconformation with respect to the C=N bond of the benzylidene moiety and have an intramolecular O—H...N hydrogen bond generating anS(6) ring motif. In the crystal, theAandDmolecules are connected by a pair N—H...S hydrogen bonds, forming a dimer with anR22(8) ring motif. In the case of moleculesBandC, they are linked to themselves by pairs of N—H...S hydrogen bonds, formingB–BandC–Cinversion dimers withR22(8) ring motifs.

In the title 1:1 adduct, C6H7N·C7H7NO2, the carboxylic acid group is twisted at an angle of 4.32 (18)° with respect to the attached benzene ring. In the crystal, the carboxylic acid group is linked to the pyridine ring by an O—H...N hydrogen bond, forming a dimer. The dimers are linked by N—H...O hydrogen bonds, generating (010) sheets.

The two independent molecules in the asymmetric unit of the title compound, C11H12Cl2N2OS, exhibit different conformations, with the benzene ring and the N2CS thiourea group forming dihedral angles of 87.40 (18) and 69.42 (15)°. An intramolecular N—H...O hydrogen bond is present in each molecule. Two further N—H...O hydrogen bonds link the independent molecules into a dimer. In the crystal, the dimers are linked by N—H...S and C—H...S hydrogen bonds, forming chains parallel to thecaxis.

In the title compound, C24H15Cl2N3O2, one quinoline ring system is essentially planar and the other is slightly bent. An intramolecular O—H...N hydrogen bond involving the hydroxy group and a pyridine N atom forms an S(5) ring motif. In the crystal, two molecules are associated into an inversion dimer with two R 2 2(7) ring motifs through intermolecular O—H...N and O—H...O hydrogen bonds. The dimers are further linked by an intermolecular C—H...O hydrogen bond and four C—H...π interactions, forming a two-dimensional network parallel to (001).

Time-dependent density functional theory (TDDFT) and second-order coupled cluster method with resolution-of-the-identity approximation (RICC2) were used to investigate the photolysis dynamics of 9-fluorenol (FOH) in alcohols. In this work, a novel mechanism for the accelerated photolysis dynamics of FOH in alcohols is proposed for the first time. The two hydrogen bonds present different effects in the dissociation process of C9–O bond in MeOH⋯FOH⋯MeOH trimer: formation of hydrogen bond MeOH⋯FOH could weaken the C9–O bond, while, hydrogen bond FOH⋯MeOH fastens the bond. Moreover, the thermodynamic equilibrium can be accomplished in both ground and excited states between hydrogen-bonded complexes, since the hydrogen bond reorganization occurs in hundreds of femtosecond upon the excitation. The excited-state potential energy (PE) curves along C9–O bond have been optimized in S1 state. The cleavage of C9–O bond upon the photoexcitation would be facilitated effectively in MeOH⋯FOH dimer. This leads the thermodynamic equilibrium between hydrogen-bonded complexes leaning to the side of MeOH⋯FOH dimer to quench the fluorescence. Therefore, the photolysis of 9-fluorenol in alcohols can be facilitated effectively by MeOH⋯FOH hydrogen bond via excited-state hydrogen bond reorganization. Additionally, the excited-state hydrogen bond reorganization is also the rate-controlling step in photolysis of FOH in alcohols, since there is no barrier in the PE curve of MeOH⋯FOH dimer.

At present, the theoretical concepts of the hydrogen bond (H-bond) in condensed media, for example, in living systems, biomolecules, are not fully solved. Quantum chemical modeling is used as one of the methods for studying the nature and determining the strength of the H-bond. In this paper, we continue to study the system of hydrogen bonds in molecular crystals of alanine and tyrosine. The dimers of these amino acids were modeled using the DFT method using the B97D functional with bases 6-31++G**. In the framework of NBO analysis, the stabilization energies of the formed hydrogen bond and the value of the transferred charge are calculated. It is shown that in alanine dimers, the main factor affecting the h-bond stabilization energy is the geometric parameters and, first of all, (N-H...O). The binding σ-orbital of the hydrogen bond is the result of the interaction of a hybrid NBO of the lone electron pairs of an oxygen atom and a loosening σ*-NBO N−H bond. The nature of bond formation in all three cases is the same, and the charge transfer value is greater than the value of the bond criterion, which indicates the presence of hydrogen bonds in all analyzed alanine systems. In tyrosine dimers, two H-bonds are formed that are similar in nature, as well as in geometric and energy parameters. The third H-bond is very weak, and the amount of charge transfer indicates its absence. The main interaction between the molecules in the third tyrosine dimer is the H-bond between the –СОО− and –OH groups. It was found that the scheme of formation of hydrogen bonds in molecular crystals of tyrosine is somewhat different from that of alanine.

A molecular recognition mechanism based on dimeric model for cyclic dipeptide Cyclo[(S)-His-(S)-Phe] (abridged CHP) catalyzed autoinduction is proposed according to the inference of previous experimental findings, which is supported by theoretical calculation with Oniom(B3LYP/3-21G*:AM1) method. The most unstable CHP dimer whose intermolecular hydrogen bonds are immensely lessened by two intramolecular hydrogen bonds is defined as the highest active component (IIa) existing in solid among the three possible dimers (Ia, IIa, and IIb). The carbonyl group of benzaldehyde coordinates to CHP dimer (IIa) by a hydrogen bond with Phe–NαH rather than His–NαH and HCN interacted with the imidazole moiety of His residue to form cyanide ion. In view of the theoretical calculation and experimental results, the structures of the nine-ring complexes derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the enantioselective autoinduction: The structure of no nitrile involved six-ring complex derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the elimination of enantioselective autoinduction.

The ternary title complex (2) is readily obtained by co-crystallization of 18-crown-6 (18C6) and di(4-carboxybenzenesulfonyl)amine (1) from hot water and was characterized by low-temperature X-ray diffraction. The crystal structure (triclinic, space group P1̄) displays one-dimensional polymeric sequences [(H2O)2···18C6···(H2O)2···{HN(SO2C6H4-4-COOH)2}2] in which the molecules are associated through seven independent hydrogen bonds. The 18C6 ring lies on a crystallographic inversion centre and adopts the common pseudo-D3d conformation. On both sides, the ring is flanked by a strongly hydrogen-bonded water dimer H2O-H-OH. This species forms three weak O-H-O bonds to alternating ether oxygen atoms and accepts a strong N-H-O bond from the adjacent acid dimer (1)2. The water dimers thus act as ideal donor-acceptor balancing links between the hexafunctional polyether and the monofunctional NH groups of the (1)2 dimers. The (1)2 dimer itself is formed by two symmetry related cyclic O-H···O interactions (both H disordered) of the well-known carboxylic acid dimer type. To this effect, molecule 1 adopts a folded, pseudo-Cs symmetric conformation with stacked carboxyphenyl groups.

Pulsed-beam Fourier transform microwave spectroscopy (PBFTMS) was used to determine the rotational structure of N-hydroxypyridine-2(1H)-thione. PBFTMS was also used to determine the rotational structure of a hydrogen dimer between propiolic acid and formic acid. Rotational constants and quadrupole coupling constants were determined. Calculations (MP2/DFT) were utilized in predicting the isotopic structures. Isotopic data (D, and ¹³C) and normal isotopomers collected were used in establishing of key structural parameters such as bond length and bond angles.

[EN] Bile acids are a family of amphiphilic steroids that play a pivotal role in physiological functions such as elimination of cholesterol or solubilization of lipids. Chemically, they share a steroidal skeleton with an unusual cis fusion between rings A and B, a short lateral chain ending in a carboxylic acid moiety and different number of hydroxyl groups on the alpha-face. Hence, bile acids offer a versatile architecture that can be used to investigate photophysical processes of interest such as hydrogen atom transfer, through-bond energy trasfer, through-bond exciplex formation and DNA photodamage-related reactions. First, unmodified bile acids have been used to evaluate hydrogen atom trasfer to benzophenone-like triplet carbonyls. Dehydrogenation of bile acids at positions C-3 and/or C-7 by a radical-mediated mechanism from the excited state of benzophenone has been demonstrated. Moreover, synthesized lithocholic acid derivatives including benzophenone or carbazole as donors and a naphthalene, biphenyl or thymine as acceptors have been employed to investigate through-bond energy transfer and exciplex formation processes. Thus, energy transfer from benzophenone to naphthalene or biphenyl and extended through-bond exciplex formation in benzophenone/naphthalene and benzophenone/biphenyl linked systems has been demostrated by laser flash photolysis. Finally, bile acid derivatives incorporating one benzophenone and two thymine units with different degrees of freedom have been prepared to investigate the photochemical formation of oxetanes or thymine dimers. Photosensitized formation of cyclobutane pyrimidine dimers through the generation of a delocalized triplet excited state has been demonstrated in intermolecular systems, while oxetane formation is observed when the degrees of freedom are reduced.
[ES] Los ácidos biliares son una familia de esteroides anfifílicos que juegan un papel clave en diferentes funciones fisiológicas tales como la eliminación del colesterol o la solubilización de lípidos. Su estructura química está constituida por un esqueleto esteroideo con una fusión cis poco común entre los anillos A y B, una cadena lateral corta que termina con una función ácida y un número variable de grupos hidroxilo en la cara alfa. Por tanto, los ácidos biliares ofrecen una estructura versátil que puede ser utilizada para investigar procesos fotofísicos de interés como abstracción de hidrógeno, transferencia de energía y formación de exciplejos a larga distancia o reacciones relacionadas con el daño fotoinducido al ADN. En esta Tesis, en primer lugar, los ácidos biliares naturales se han utilizado para evaluar la abstracción de hidrógeno a carbonilos triplete en compuestos derivados de la benzofenona, demostrándose la deshidrogenación de los ácidos biliares en las posiciones C-3 y/o C-7 por un mecanismo radicalario desde el mencionado triplete de la benzofenona. En segundo lugar, se han preparado derivados de ácido litocólico que incluyen los dadores benzofenona o carbazol y los aceptores naftaleno, bifenilo o timina, que a continuación se han utilizado para investigar los procesos de transferencia de energía y formación de exciplejo intramolecular a larga distancia. De hecho, en los sistemas benzofenona/naftaleno y benzofenona/bifenilo, se demostró por fotólisis de destello láser la transferencia de energía desde benzofenona a naftaleno o bifenilo y la formación de exciplejo a larga distancia. Por último, se han preparado derivados de ácidos bliares que incorporan una unidad de benzofenona y dos de timina en diferentes posiciones del esqueleto para investigar la influencia de los diferentes grados de libertad en la formación fotosensibilizada de oxetanos o dímeros de timina. Gracias a ellos, se ha demostrado la formación fotosensibilizada de dímeros ciclobutánicos pirimidínicos a través de la generación de estados excitados triplete deslocalizados en sistemas en los que la benzofenona es intermolecular, mientras que se observa formación de oxetanos cuando los grados de libertad se ven reducidos.
[CAT] Els àcids biliars són una família d'esteroides anfifílics que juguen un paper clau en funcions fisiològiques com l'eliminació del colesterol o la solubilització de lípids. La seua estructura química està constituïda per un esquelet esteroïdal amb una fusió cis entre els anells A i B poc comuna, una cadena lateral curta que acaba amb una funció àcida i un nombre diferent de grups hidroxil en la cara alfa. D'aquesta manera, els àcids biliars ofereixen una estructura versàtil que pot ser utilitzada per investigar processos fotofísics d'interès com abstracció d'hidrogen, transferència d'energia i formació de exciplexes a llarga distància o reaccions relacionades amb el dany a l'ADN induït per llum. En primer lloc, els àcids biliars naturals s'han utilitzat per avaluar la abstracció d'hidrogen a carbonils triplets derivats de la benzofenona, demostrant-se la deshidrogenació dels àcids biliars en les posicions C-3 i/o C-7 per un mecanisme radicalari des de l'estat excitat de la benzofenona. A més, derivats d'àcid litocòlic que inclouen els donadors benzofenona o carbazol i els acceptors naftalé, bifenil o timina s'han utilitzat per investigar els processos de transferència d'energia i formació de exciplexe a llarga distància. En els sistemes benzofenona /naftalé i benzofenona/bifenil la fotòlisis làser va demostrar la transferència d'energia des de benzofenona a naftalé o bifenil i la formació d'exciplexe a llarga distància. Finalment, per tal d'investigar la formació fotosensibilitzada d'oxetans o dímers de timina, s'han preparat derivats d'àcids bliars que incorporen una unitat de benzofenona i dues de timina amb diferents graus de llibertat. La formació fotosensibilitzada de dímers ciclobutànics pirimidínics mitjançant la generació d'estats excitats triplet deslocalitzats ha estat demostrada en sistemes intermoleculars, mentre que la formació d'oxetans s'observa quan els graus de llibertat es veuen reduïts.
Miró Richart, P. (2016). Hydrogen-Abstraction, Energy Transfer and Exciplex Formation in Photoactive Systems Based on Bile Acids [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/64084
TESIS

En stor samling dimolekylära vätebindningar med formen A – H … B, där AH är en alkyn, alkohol eller tiol och B = [Br–, Cl–, NH3, HCN] beräknas och utvärderas med Kohn-Sham täthetsfunktionalteori tillsammans med bassetet m062x/6-311+g(2df.2p). Dessa komplex utvärderas även med en punktladdningsmodell (som använder samma metod och basset), där atomerna i vätebindningsmottagaren B byts ut mot laddningar som passats för att återskapa laddningsfördelningen runt molekylen, med målet att separera och isolera de elektrostatiska och polariserande energikomponenterna från de totala interaktionsenergierna. Med hjälp av detta tillvägagångssätt visade det sig att vätebindningars komplexeringsenergi (i.e. interaktionsenergin med energikostnaden för att deformera atomkärnornas rymdgeometri borttagen), oberoende av karaktären hos monomeren AH eller B, till stor del består av elektrostatik och polarisation, medan laddningsutbyte, dispersion, och andra resttermer endast utgör en liten del av den totala interaktionen. Fördelningen mellan elektrostatik och polarisation varierar beroende på typen av monomerer i vätebindningen, men deras summa, den resulterande punktladdningsenergin, korrelerar linjärt (ΔECompl = 0.85ΔEPC ) med R2 = 0.995 över energiomfånget 0 < ΔECompl < 50 kcal mol–1. Detta blir ännu mer anmärkningsvärt då inkluderingen av komplexeringsenergierna från halogenbindningar i samma korrelation inte förändrar korrelationskoefficienten avsevärt, vilket indikerar att båda bindningstyperna består av samma energikomponenter även då bindningarna i sig är väldigt olika.
A large set of dimeric hydrogen bonds of the type A – H … B, where AH is an alkyne, alcohol, or thiol and B = [Br–, Cl–, NH3, HCN]  are computed and evaluated using Kohn-Sham density functional theory together with the m062x/6-311+g(2df.2p) basis set. These complexes are also evaluated using a point charge (PC) approach (using the same method and basis set), where the atoms of the hydrogen bond acceptor B are substituted for charges that are optimized to reproduce the charge distribution of the molecule, with the purpose of separating and isolating the electrostatics- and polarization energy components of the interaction energies. Using this approach it was discovered that the complexation energy of hydrogen bonds (i.e.the interaction energy with the energy cost of nuclear deformation corrected for), independent on the nature of either monomer AH or B, are largely made up of electrostatics and polarization, while charge transfer, dispersion, and other rest terms only make up a small fraction of the total interaction. The composition of electrostatics and polarization vary depending on the type of monomers in the hydrogen bond, but their sum, the PC interaction energy, correlates linearly (ΔECompl = 0.85ΔEPC )  with R2 = 0.995 over an energy span of 0 < ΔECompl < 50 kcal mol–1. This is made even more remarkable by the inclusion of halogen bonded complexation energies in the same correlation without changing the correlation coefficient significantly, indicating that the two bond types are comprised of the same components even though they are remarkably different in origin.

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.

Ma Nap Tak.
Thesis submitted in: December 2004.
Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.
Includes bibliographical references (leaves 109-114).
Abstracts in English and Chinese.
ABSTRACT (ENGLISH) --- p.iii
ABSTRACT (CHINESE) --- p.iv
ACKNOWLEDGMENTS --- p.v
ABBREVIATION --- p.vi
TABLE OF CONTENTS --- p.vii
LIST OF FIGURES --- p.x
LIST OF TABLES AND GRAPHS --- p.xii
Chapter CHAPTER 1 --- Introduction and Background --- p.1
Chapter 1.1 --- Introduction --- p.1
Chapter 1.2 --- Hydrogen bonds (H-bonds) in DNA --- p.2
Chapter 1.2.1 --- Experimental Evidences of Hydrogen Bonding --- p.3
Chapter 1.3 --- Three-centered hydrogen bond (TCHB) --- p.4
Chapter 1.3.1 --- Definition of Three-centered hydrogen bond (TCHB) --- p.5
Chapter 1.3.2 --- Significance of Three-centered hydrogen bond (TCHB) --- p.6
Chapter 1.3.3 --- Characterization of Three-centered hydrogen bond (TCHB) --- p.7
Chapter 1.3.4 --- Classification of Three-centered hydrogen bond (TCHB) --- p.7
Chapter 1.4 --- Charge transfer in DNA --- p.9
Chapter 1.4.1 --- Theory of DNA charge transfer --- p.9
Chapter 1.4.2 --- Short and long range hole transfer in DNA --- p.10
Chapter 1.4.3 --- Electron transfer in DNA --- p.12
Chapter 1.4.4 --- Summary of DNA charge transfer --- p.12
Chapter 1.5 --- Thesis Scope --- p.13
Chapter CHAPTER 2 --- Theory and methodology --- p.16
Chapter 2.1 --- Introduction --- p.16
Chapter 2.2 --- Theory --- p.17
Chapter 2.2.1 --- Density Functional Theory (DFT) --- p.17
Chapter 2.2.2 --- Basis set selection --- p.18
Chapter 2.2.3 --- Natural Bond Orbital (NBO) --- p.19
Chapter 2.2.3.1 --- Natural Population Analysis (NPA) --- p.20
Chapter 2.2.3.2 --- E(2) --- p.20
Chapter 2.2.3.2 --- bond index --- p.21
Chapter 2.2.4 --- spin-spin coupling constants --- p.22
Chapter 2.2.5 --- Molecular Orbital (MO) --- p.23
Chapter 2.3 --- Methodology --- p.24
Chapter 2.3.1 --- Test calculation for TCHBs by NBO --- p.24
Chapter 2.3.2 --- Geometry Optimization --- p.24
Chapter 2.3.3 --- NBO analysis --- p.25
Chapter 2.3.4 --- J-coupling constants (lhJnx) and MO calculations --- p.26
Chapter 2.4 --- Summary --- p.26
Chapter CHAPTER 3 --- Results and Discussion --- Hydrogen bonding in DNA --- p.27
Chapter 3.1 --- Introduction --- p.27
Chapter 3.2 --- Method for extracting DNA dimer models --- p.27
Chapter 3.3 --- Computed results of Inter H-bonds of the ten dimer models --- p.33
Chapter 3.3.1 --- Geometric parameters --- p.33
Chapter 3.3.2 --- Natural Bond Orbital (NBO) Analysis --- p.36
Chapter 3.3.2.1 --- E(2) and Wiberg Bond index --- p.36
Chapter 3.3.2.2 --- The relationship of E(2) and bond distance --- p.40
Chapter 3.3.2.3 --- The relationship of E(2) and bond angle --- p.42
Chapter 3.3.2.4 --- The relationship of E(2) and bond index --- p.44
Chapter 3.3.3 --- Spin-Spin Coupling Constants of inter-H bonds --- p.46
Chapter 3.3.3.1 --- The relationship of spin-spin coupling constant and distance --- p.49
Chapter 3.3.3.2 --- The relationship of spin-spin coupling constant and bond angle --- p.50
Chapter 3.3.3.3 --- The relationship of spin-spin coupling constant and E(2) energy --- p.52
Chapter 3.4 --- Experimental Characterization of Three-centered H-bonds --- p.54
Chapter 3.5 --- Theoretical Characterization of Three-centered H-bonds --- p.55
Chapter 3.5.1 --- Geometry properties (360°C Rule) --- p.55
Chapter 3.5.2 --- NMR properties (Spin-Spin Coupling Constants) --- p.55
Chapter 3.5.3 --- NBO properties (E(2) and Wiberg bond index) --- p.56
Chapter 3.6 --- Computed results of Three-centered hydrogen bonds (TCHBs) of the ten dimer models --- p.56
Chapter 3.6.1 --- Natural Bond Orbital (NBO) Analysis --- p.56
Chapter 3.6.1.1 --- Determination of TCHBs in the ten dimer models --- p.56
Chapter 3.6.1.2 --- Analysis of TCHB interactions (E(2) and bond index) --- p.62
Chapter 3.6.1.3 --- The relationship between E(2) and bond distance of TCHBs --- p.63
Chapter 3.6.1.4 --- The relationship between E(2) and bond angle of TCHBs --- p.65
Chapter 3.6.2 --- Spin-Spin Coupling Constants of TCHBs --- p.66
Chapter 3.6.2.1 --- The relationship between spin-spin coupling constant and bond distance of TCHBs --- p.68
Chapter 3.6.2.2 --- The relationship between spin-spin coupling constant and E(2) energy of TCHBs --- p.69
Chapter 3.6.3 --- Geometry of TCHBs --- p.71
Chapter 3.7 --- Summary --- p.72
Chapter CHAPTER 4 --- Results and Discussion --- Charge location and charge transfer in DNA --- p.77
Chapter 4.1 --- Introduction --- p.77
Chapter 4.2 --- Method --- p.78
Chapter 4.3 --- Computed results of the charge location of the trimer models --- p.81
Chapter 4.3.1 --- Location of excess positive charge --- p.81
Chapter 4.3.2 --- Location of excess negative charge --- p.90
Chapter 4.4 --- Role of TCHBs in charge transfer --- p.95
Chapter 4.4.1 --- Introduction --- p.95
Chapter 4.4.2 --- "Analysis of G1G2C3, C3A4A5 and A8A9C10 trimers" --- p.96
Chapter 4.4.3 --- Analysis of A7A8A9 and A8A9C10 trimers --- p.103
Chapter 4.5 --- Summary --- p.105
Chapter CHAPTER 5 --- Concluding Remarks --- p.107
REFERENCES
APPENDIX

Mass-selected infrared multiple photon spectroscopy (IRMPD), Fourier transform ion cyclotron resonance (FT-ICR) kinetic experiments, RRKM and electronic structure calculations have been performed in order to propose a complex mechanism involving the formation of the proton-bound dimer of water (H5O2+) from 1,1,3,3-tetrafluorodimethyl ether. It has been found that the reaction is facilitated by a series of sequential exothermic bimolecular ion-molecule reactions. Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate which decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). The 1,4-elimination of hydrogen fluoride is found to be strongly supported by the results of both RRKM theory and electronic structure calculations. Lastly, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition and product species was obtained using MP2/aug-cc-pVQZ//MP2(full)/6-31G(d) level of theory. Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and two of the protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. It was found that the formation of a proton-bound dimer (PBD) of caffeine and ammonia was elusive under the experimental conditions. The low binding energy of the caffeine and ammonia PBD is responsible for the perceived difficulty in obtaining an IRMPD spectrum. The IRMPD spectrum of the PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also obtained. The spectrum of protonated caffeine showed the dominant existence of a single isomer, whereas the spectrum of protonated theophylline showed a mixture of isomers. The mixture of isomers of protonated theophylline resulted as a consequence of proton-transport catalysis (PTC) occurring within the PBD of theophylline and ammonia. All calculated harmonic spectra have been produced at the B3LYP/6-311+G(d,p) level of theory with fundamental frequencies scaled by 0.9679; calculated anharmonic spectra have also been provided at the same level of theory and were found to greatly improve the match with the IRMPD spectra obtained in all cases. Ionic hydrogen bond (IHB) interactions, resulting from the association of caffeine and theophylline with their protonated counterparts, forming proton-bound homodimers, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. It is found that the IRMPD spectra of the proton-bound homodimers of caffeine and theophylline are complicated resulting from the existence of several pairs of enantiomers separated by a narrow range of relative Gibbs free energies (298 K) of 15.6 and 18.2 kJ mol-1, respectively. The IRMPD spectrum of the proton-bound homodimer of theophylline is dominated by a unique isomer facilitated by formation of a bidentate IHB. Formation of this interaction lowers the relative Gibbs free energy of the ion to 9.75 kJ mol-1 below that of the most favourable pair of enantiomers. The IRMPD spectrum of the PBD of caffeine is complicated by the existence of at least two pairs of enantiomers with the strong likelihood of the spectral contributions of a third pair existing. The most favourable enantiomeric pair involves the formation of a O-H+⋯O IHB. However, verification of a pair of enantiomeric PBDs containing a N-H+⋯O IHB is also observed in the IRMPD spectrum of the PBD of caffeine due to the presence of three free carbonyl stretching modes located at 1731, 1751 and 1785 cm-1. The mass-selected IRMPD spectra of the sodium cation-bound dimers (SCBD) of caffeine and theophylline also have been obtained. Both the mass-selected IRMPD spectra and electronic structure calculations predict the most likely structure of the SCBDs of caffeine and theophylline to form by an efficient O⋯Na+⋯O interaction between C=O functional groups possessed by each monomer. The frequencies of the C=O-Na+ stretch are found to be nearly identical in the IRMPD spectra for both of the SCBDs of caffeine and theophylline at 1644 and 1646 cm-1, respectively. However, the degenerate free C=O symmetric and asymmetric stretches for the SCBDs of caffeine and theophylline found at 1732 and 1758 cm^(-1), respectively, demonstrating a red-shift for caffeine possibly linked to a steric interaction absent in theophylline. Free rotation about the O⋯Na+⋯O bond is found to greatly decrease the complexity of the IRMPD spectra of the SCBDs of caffeine and theophylline and demonstrates excellent agreement between the IRMPD and calculated spectra. Electronic structure calculations have been done at the MP2(full)/aug-cc-pCVTZ/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory using the aug-cc-pCVTZ basis set for Na+ and all Na+-interacting heterotatoms, and the 6-311+G(2d,2p) basis set for all non-interacting atoms within the SCBDs, in order to provide accurate electronic energies. Currently, installation and implementation of a pulsed electrospray high pressure ion source mated to an existing high pressure mass spectrometer (HPMS) is underway. The new ion source will greatly increase the range of possibilities for the study of ion-molecule reactions in the McMahon laboratory. One of the unique features of the new design is the incorporation of a gas-tight electrospray interface, allowing for more possibilities than only the study of cluster-ion equilibria involving hydration (H2On⋯S+), where S+ is an ion produced by electrospray. Other small prototypical biological molecules such as amines and thiols can be used without concern for the toxicity of these species. Another unique design feature allows electrosprayed ions to associate with neutral solvent species in an electric field free reaction chamber (RC). This ensures that values of equilibrium constants determined are truly representative of ions in states of thermochemical equilibrium. The existing HPMS in the McMahon laboratory is limited to the study of small volatile organic molecules. The new ion source will permit the exploration of systems involving non-volatile species, doubly charged ions and many biologically relevant molecules such as amino acids, peptides, nucleobases and carbohydrates.

Human normal adult hemoglobin (Hb) A, the oxygen carrier of blood, is a tetrameric protein consisting of two α chains of 141 amino acid residues each and two β chains of 146 amino acid residues each. Each Hb chain contains a heme group which is an iron complex of protoporphyrin IX. Under physiological conditions, the heme-iron atoms of Hb remain in the ferrous state. In the absence of oxygen, the four heme-irom atoms in Hb A are in the highspin ferrous state [Fe(II)] with four unpaired electrons each. Each of the four heme-iron atoms in Hb A can combine with an O2 molecule to give oxyhemoglobin (HbO2) in which the iron atom is in a low-spin, diamagnetic ferrous state. The oxygen binding of Hb exhibits sigmoidal behavior, with an overall association constant expression giving a greater than first-power dependence on the concentration of O2. Thus, the oxygenation of Hb is a cooperative process, such that when one O2 is bound, succeeding O2 molecules are bound more readily. Hb is an allosteric protein, i.e., its functional properties are regulated by a number of metabolites [such as hydrogen ions, chloride, carbon dioxide, 2,3-diphosphoglycerate (2,3-DPG)] other than its ligand, O2. It has been used as a model for allosteric proteins, and indeed, hemoglobins of vertebrates are among the most extensively studied allosteric proteins. Their allosteric properties are physiologically important in optimizing O2 transport by erythrocytes. The large number of mutant forms of Hb available provides an array of structural alterations with which to correlate effects on function. For details, see DickersonandGeis (1983), Bunnand Forget (1986), Ho (1992), Ho and Perussi (1994). There are two types of contacts between the α and β subunits of Hb (Perutz, 1970; Dickerson and Geis, 1983). The α1β1 (or α2 β2) contacts, involving B, G, and H helices, and GH corners, are called packing contacts. These contacts remain unchanged and hold the dimer together even when there is a change in the ligation state of the heme.