Structure of Water and Its Dynamic Hydrogen Bond Network

Structure of Water and Its Dynamic Hydrogen Bond Network Introduction Water is essential to life as it is main constituent of cell in living organism. All biological macromolecules are almost inactive in its structural stability and functioning in absence of water. Water-Role in Life Water is key compound for our existence on this planet due to its ubiquitous presence on the earth and in living organisms. It is involved in all chemical, biological and geological processes. Due to its anomalous behavior it named as ‘matrix of life’, ‘solvent of life’. It plays a vital role from molecule and cell to tissues and organisms.1-4 In past several decades water has attracted the most scientific attention among the liquid due to its anomalous properties. It shows peculiar properties such as negative volume of melting, density maximum at 277 K, high melting and boiling point, high dielectric constant, minimum in the isobaric heat capacity and isothermal compressibility at 308 K and 319 K, respectively, high mobility transport for H+ and OH ions. The density of most liquids increases as it freeze but in case of water it expands about 11% due to which ice floats on water. It is the solvent of life and plays an important role in protein interactions a nd stabilization of protein structure. The work of Kauzmann gives the importance of water in protein folding and its interactions with water.5 Structure of Liquid Water The anomalous behavior of water is due to its unique ability to form a network of self associated molecules through hydrogen bonding. To study the structure of water and its dynamic hydrogen bond network large number of studies has been carried out.1-12 Still many aspects of water are not fully understand at molecular level. Dyke and co-workers first reported existence of H-bonding in vapor phase experimentally and measured the H-bond length as 2.98 Ã… in water dimer using molecular beam resonance technique which is higher than water in solid (for ice H-bond strength 2.74 Ã…) and liquid (2.85 Ã…) indicates the H-bond strength is weaker in Gas phase.13 From X-ray diffraction study of Bernal and Fowler and Morgan and Warren it is revealed that water is tetrahedrally coordinated through hydrogen bonds similar to the structure of ice I (Figure 1.1). 14-15The number of theories for the water structure has been proposed based on different techniques such as X-ray, neutron diffraction, dielectric relaxation and Raman spectroscopy. 16-22. These theories are generally classified into two models as a) Continuum model and b) Mixture model. Figure 1.1 Crystal structure of ice I at low pressure Continuum model In continuum model it is assumed that almost completely hydrogen bonded water molecules in a continuous network. Pople described the continuum model which is agreement with the observed variation of X-ray radial distribution function with temperature. 23According to Pople In continuous bonded network of the water bond bending and deformations occurs instead of bond water. Recently, Rice and Sceats 24proposed Random Network Model (RNM), which explains the continuum model and it is further developed by Henn and Kauzmann. 25This model is used for determining the heat capacity contribution due to water-water interactions. b) Mixture model In mixture model water consists of differently H-bonded species with zero, one or both hydrogens are engaged in hydrogen bonding. Franks and Wen 26 gives the â€Å"Flickering Cluster† model in which cooperative H-bonding is observed in water molecules. The co-operativity involves the hydrogen bond formation of one bonding site of water molecule contributes the delocalization energy to the molecule, which is involved in hydrogen bonding with another water molecule. According to Franks and Wen the clusters of the water molecules (bulk water) and free monomer molecules (dense water) are in equilibrium with each other. Samoilov 27 proposed the interstitial model in which water molecules are present in the cavities of ice lattice. Nemethy and Scheraga 28 used statistical thermodynamic model to calculate the Helmholtz free energy, internal energy and entropy as a function of temperature. Also the water hydrate model proposed by Pauling. 29 Now a days, theoretical techniques such as Monto Carlo, molecular dynamic simulation are used to study structural behavior of water. It provides most promising approach for the study of water at molecular level. Jorgensen 30 has developed transferable intermolecular potential functions (TIPS) suitable for use in liquid simulations for water. This potential has been used by Jorgensen and Madura 31 in MC simulation on liquid water to study the effect of temperature on vaporization, hydrogen bonding, density, isothermal compressibility and radial distribution functions. Number of water models such as SPC, TIP3P, TIP4P, TIP5P are developed for the molecular simulation of large biomolecular systems. Figure 1.2 Frank-Wen Flickering Cluster Model of Liquid Water 1.2 Hydrophobic Hydration and Hydrophobic Interactions The weak non-covalent interactions like van der Waals forces, H-bonding, ion-dipole, hydrophobic interactions are responsible for change in the structure of water around the solute molecule. The hydrophobic interaction is the prominent factor in the solvation of apolar or non-polar molecule. When a non-polar solute is dissolve in water there is large negative change in entropy. The disruption in the normal H-bonded structure is occurred and new H-bonded cage-like structure is formed around the solute molecule. So the structure formed is more ordered than the ordinary water. The term hydrophobic hydration is used when non-polar solute solvated by the cage of the solvent molecule around it. The short lived aggregates are formed around the solute molecule. The formation of polymeric aggregates strengthens the hydrogen bonding which gives negative contribution to ΔH0. 10 The hydrophobic interactions are important in a field of biochemistry for the purpose of conformational stability of biological macromolecules, protein folding, aggregation, ion transport, drug delivery as well as in industry. Usually hydrophobic hydration occurs in non-polar compounds such as alcohols, ethers, and amines. The tetraalkylammonium (TAA) salts with larger cation also shows the hydrophobic hydration effect. Kustov gives the effect of size of cation on the hydrophobic hydration. He studied the specific heat of solution for the higher size cation TAA salts and observed that as the size of cation in salt increases the specific heat of solution and hydration increases upto the tetrapentylammonium salts and then decreases. As the specific heat of solution increases the hydrophobic hydration increases. For the hexyl and heptyltetraalkylammonium salts the ΔC0p decreases so the hydrophobic hydration weakens. Thus hydrophobic hydration depends on the size of cation of TAA. Th e hydrophobic interaction is best explained by Goring et al. by studying the interaction of non-electrolytes in aqueous solutions by dilatometrically. They compared the apparent specific volume (à Ã¢â‚¬ ¢2) relative to apparent specific volume at 0  ºC as function of temperature for non-electrolytes and showed that 1-butanol behaves like hydrophobic compound and acts as structure maker in aqueous solution while glycerol with polar groups disrupts the structure of water. The hydrophobic compound shows the slope dà Ã¢â‚¬ ¢2/dT is less than the corresponding thermal expansions of pure compound while it greater for the hydrophilic compounds. Madan and Sharp explained that non-polar solutes have large capacity heat of hydration ΔCp while for polar solutes it is small negative. The large change in heat capacity at high temperature is due to unfavorable enthalpic interacions and not due to entropy change. The effect of salt on the hydrophobic hydration was carried out by Talukdar and Kundu and observed that hydrophobic cation induce more hydrophobic hydration in aqueous NaNO3 solution than in pure water. Rossky et al. with the help of computer simulation studied the hydration properties of the interfaces between the water and the hydrophobic surfaces for the active peptide melittin in its monomeric and dimeric form and concluded that hydrophobic hydration is depends on the surface topography of biomolecule. 1.3 Spectroscopic study of water Due to its various anomalous properties and great importance in the several field water is the most studied compound. To study the structure of water, number of spectroscopic techniques such as IR, Raman, neutron diffraction, X-ray scattering, NMR spectroscopy etc. have been used still today. The spectroscopy and scattering studies provides the structural information of water at molecular level. Bernal and Fowler analyzed the X-ray diffraction of water and investigated water as distorted quartz-like. The hydrogen bond network in water is found to be tetrahedral in nature and each water molecule can be bound with another four water molecules i.e. each water molecule is double proton donor and double proton acceptor. While recently, Wernet et al. studied the structure of water by soft X-ray absorption spectroscopy and X-ray Raman scattering and investigate that hydrogen bond network in the water consists of only two strong hydrogen bonds and one act as proton door and another as proton acceptor. This controversial result of structure of water from earlier study makes the scientist to study the water structure more interesting. In this context, number of scientists have been studied the water structure by X-ray absorption spectroscopy. Infrared and Raman techniques are also the important sources of the information of hydrogen bonding in water. Above the absolute temperature all the atoms in the molecules are in continuously vibrating motion with respect to each other. Any molecule absorbs the radiation when frequency of a specific vibration is equal to frequency of the IR radiation directed on the molecule. Each atom has three degrees of freedom, corresponding to motions of the three Cartesian coordinate axes (x, y, z). Total no of coordinate values is 3N for a molecule containing N atoms. Thus, Water has 9 degrees of freedom with C2v symmetry. It shows the two stretching vibrations (symmetric and asymmetric), one bending vibration, three hindered rotations (librations), and three hindered translations. Earlier, number of research papers has been published on the study of the structure of water in solid, liquid as well as in vapor phase by IR and Raman technique. The fundamental IR frequencies for the H2O and heavy water is as shown in Table Table: Fundamental vibrations of liquid ordinary water and heavy water Vibration(s) liquid H2O (25  °C) liquid D2O (25  °C) liquid T2O v, cm-1 ÃŽ µÃŽ », M-1cm-1 v, cm-1 ÃŽ µÃŽ », M-1cm-1 v, cm-1 v2 1643.5 21.65 1209.4 17.10 1024 combination ofv2+ libration 2127.5 3.46 1555.0 1.88 v1,v3, and overtone ofv2 3404.0 100.61 2504.0 69.68 2200 http://www1.lsbu.ac.uk/water/water_vibrational_spectrum.html Walrafen investigated the structure of water by Raman spectroscopy in the intermolecular as well as intramolecular vibrational region. From Raman scattering it is observed that for liquid H2O and D2O a broad weak hydrogen bending band at 60 cm-1 and it is observed to be decreases as temperature rise, the band near 170 cm-1 is produced by the stretching motion of O-H band in water molecule. This is also decreases as increases in temperature which indicates the structural breakdown of water units. These vibrations are the intermolecular vibrations of water which are observed in the restricted translational region. The intramolecular vibrations of water occurs in the range of 2000-4000 cm-1.Walrafen studied the Raman spectra of 50 mole % solution of H2O and D2O in the intramolecular region in which principle contribution of HDO vibrations are studied. The two maxima at 3415 ±5 cm-1 and 2495 ±5 cm-1 are referred due to OH and OD stretching vibrations of HDO, and of H2O and D2O. Also the weak band at 2860 ± 10 cm-1 arises from the overtone of the fundamental intramolecular bending vibration of HDO near 1450 cm-1. When H2O, D2O mixture studied at 32.2 to 93  ºC, the isosbestic point observed at 2570 ±5 cm-1 indicates the equilibrium exists between hydrogen bonded and nonhydrogen bonded OD stretching vibrations. Senior and Verrall observed same results when studied the HDO stretching at temperature 29 to 87  ºC by infrared spectroscopy. Bakker et al. studied the lifetime of the OH-stretching vibration in the water as a function of temperature by using femtosecond mid-infrared pump-probe spectroscopy and observed that it increases from 260 ±18 (at 298 K) to 320 ±18 (at 358 K) Recently, molecular dynamic simulation is becomes the fast method for the structural detection at molecular level. Xantheas et al. used the ab initio method to obtain the vibrational frequencies as well as zero point energy for the water clusters and its isomers with the help of second-order Mà ¸ller–Plesset perturbation level of theory (MP2) with the augmented correlation consistent basis set of double zeta quality (aug-cc-pVDZ). 1.3.1 Near-Infrared spectral study of water and aqueous solutions Near-Infrared consists of the region 800-2500 nm (12500-4000 cm‑1) in the electromagnetic spectrum. In this region molecule have energy sufficient to excite first (2ÃŽ ½), second (3ÃŽ ½), and higher overtones (nÃŽ ½) vibrations. The overtones observed in the molecule when the intermolecular vibrations of the molecules do not obey the Hook’s law. The band is more intense when the greater the anharmonicity. The combination bands are also observed in the same region. Near infrared spectroscopy is the basic tool to study the hydrogen bonding in molecule. Earlier, the scientist Luck studied water and alcohol in the NIR region and observed that the strength of cooperativity of H-bond in water is about 250 % stronger than H-bond in a monomeric water. Different species of water present in the cooperative H-bond such as H-non bonded, H-bond strong and H-bond weaker. Ozaki et al. studied the structure of water by using two analytical techniques such as two dimensional correlation spectroscopy and principal component analysis in which they showed the two-state water model by measurements of the water at different temperatures from 6 to 80  ºC. Two bands are observed at 1412 and 1491 nm due to two different species of water i.e. weak H-bond and strong H-bond respectively. The species observed at 1438 nm which has no much effect of temperature which suggested may be due to distorted two-state model of water. The water at high temperature and pressure rem arkably exhibits different properties than at ambient temperature. It becomes good solvent for hydrophobic substance such as benzene and hydrocarbons which are non-polar gets completely miscible at certain temperature and pressure. The effect of high temperature as well as pressure has been given by Ikawa et al. in the range of 5500 to 7800 cm-1. They observed the band at 7000 cm-1 gradually shifts to higher wavenumber is due to free OH vibrations and at 673 K and 400 bar pressure the absorption band retain the rotational features i.e. water molecule quite rotate freely though there is collision with other molecules. Recently, Near-Infrared spectroscopy has been used extensively for chemical analysis and characterization. The applications of NIR spectroscopy in various fields have attracted the scientific community. It is also used in the determination of moisture content in food samples. It can be used to probe the hydration effects in aqueous solutions of salt. Wu et al. have studied the effect of ethanol on the structural organization of aqueous solutions of [Bmim][BF4] and [Amim][Cl] using one-dimensional and 2D correlation NIR spectroscopy. They showed that hydrogen bonding between water and ILs gets reduced in presence of high concentration of ethanol32 and can be used to remove water as an impurity in hygroscopic ILs. They also used this technique to study aggregation behavior of ILs in water. NIR spectroscopy has been used previously for the study of hydration by McCabe and Fisher in which they have studied the hydration of perchlorate and alkali halides in aqueous solutions by using excl uded volume. Koga et al. have given the excess molar absorptivity in the range of 4600-5500 cm-1 i.e. (ÃŽ ½2+ÃŽ ½3) combination band of water for the Na halides and concluded that the Br‑ and I form the hydrogen bond directly with the water network which is different than the Cl ion. Bonner and Woolsey have obtained the hydration number for some alkali halides by using the 958 nm (2ÃŽ ½1+ÃŽ ½3) combination band of water. By applying their method, Hollenberg et al. calculated the hydration number for amino acids and carbohydrates The new concept introduced by Noda in 1993 i.e. two dimensional correlation spectroscopy has attracted many scientist to study effect of solutes on the structure of water by IR as well as NIR spectroscopy. This technique becomes powerful tool for the elucidation of spectral changes induced by temperature, time and concentration. Noda et al. studied the structural and crystallization dynamics of poly(L-lactide) during isothermal cold crystallization by two dimensional correlation spectroscopy. An interpretation of the evolution with temperature of the ÃŽ ½2+ÃŽ ½3 combination band in water V. Fornà ©s and J. Chaussidon, J. Chem. Phys. 68, 4667-4671 (1978) Near-infrared spectroscopic study of water at high temperatures and pressures Yusuke Jin and Shun-ichi Ikawa J. Chem. Phys., 119(23), 12432-12438, 2003. The importance of cooperativity for the properties of liquid water W.A.P. Luck Journal of Molecular Structure, 448 (1998) 131 142. Studies on the Structure of Water Using Two-Dimensional Near-Infrared Correlation Spectroscopy and Principal Component Analysis V. H. Segtnan, S. Sasic, T. Isaksson, Y. Ozaki Anal. Chem. 2001, 73, 3153-3161

Life and Death :: essays research papers

Throughout history man has made many journeys, far and wide, Moses great march though the Red Sea and Columbus’ crossing of the Atlantic Ocean are only a few of mans greatest voyages. Even today great journeys are being made. In every instances people have had to rise above themselves and over come emence odds. The Joads did just that by traveling to California to find work. Steinbeck shows one aspect of this real life journey by displaying it by a turtle and it’s struggle to reach the other side of a road. As the turtle is about to reach his goal, it is returned to it’s original location, but it does not waver in it’s determination, and continues across the road until it reaches the other side. The Joad family and Casy identify with this the most because the undergo tremendous heartache, yet they stay true to their plans and never give up. They are faced with death and sickness, but they never give up. Steinbeck wrote â€Å"In the evening a strange thin g happened: twenty families became one family, the children were the children of all the loss of home became one loss, and the golden time in the West was one dream† This was what the Joads were searching for they wanted to feel like they belonged. Ma was the one who was mostly searching for this. This is her journey to keep the family together. Her belief that a broken-family will not be able to accomplish anything. This is displayed by her not allowing the two cars to split and arrive at California at different times, when one of the cars breaks down, as they are leaving Oklahoma. Ma says â€Å"I ain’t a-gonna go.† The only way she’ll let the family break up is if pa whips her and makes her go. Pa’s journey is displayed by his trying to fit in and make a difference. He does not handle this move very well, and throughout their journey, he is confused, and not as headstrong as Ma. He realizes this also, he knows that he can’t help the family the way he use to. So he searches for anyway he can help. When the rain was coming it was this idea to dig a ditch. It was a good idea but it failed and it reflected on him. Tom Joad is a very complicated individual, who is a tremendous asset and at the same time a tremendous burden.

Philosophical Analysis Essay

â€Å"In the case of an ordinary illusion of the senses we often say: This object seems thus or so; but in reality it is thus †¦ (but) the seeming is opposed to the reality only in so far as the chance experience of one point of view gets contrasted with what would be, or might be, experienced from some larger, more rationally permanent, or more exclusive and uniting point of view. † Truth is the embodiment of reality; reality is the embodiment of experience. Yet, truth and reality are problematic concepts. Reality, when expressed in categorical terms, is in itself manifest-creating concept; that is, there is no clearly defined boundary of finding the essence of entities. In short, an attempt to define reality will result to more questions. An attempt to examine the source or basis of reality will inevitably result to ambiguity. What is the implication of this fact to truth? Truth also becomes a manifest-creating concept. Its basis is, from a vantage point, a derivation of reality (Kant, 1786/1926). Here, there is a need to mention two bases of truth and reality. For some philosophers, reality and truth are generally derived from sense experience. Aristotle once argued that the fundamental basis of reality is actual reference to existing objects. Here, reality is objective; truth is absolute. For other philosophers, rationality rather than sense experience is the formal basis of reality. Descartes, for example, argued that sense experiences often result to disconcerting assumptions of what is real and ought to be real (Descartes, 1637/1999). An example may suffice this point. Suppose an individual sees an oar in the water. From sense experience, the individual will interpret the phenomenon as genuine phenomenon. However, the individual perception of what is real is compounded by illusory assumption of what ought to be real. Descartes argued that the oar in the water, when rationality is used as means to discern truth, is a reflection of an actual oar. 2) â€Å"The best definition of truth from a logical standpoint is that which is fated to be ultimately accepted by all investigators †¦ (and not something to be identified with) some purely personal end, some profit upon which a particular individual has set his heart. † For many centuries, philosophers pondered on the best definition of truth. Perhaps, the most influential philosopher who developed a systematic approach in analyzing the nature of truth is Immanuel Kant. According to Kant, truth in categorical definition is a derivation of collective facts (Kant, 1786/1926). Kant argued that when a set of facts are accepted to be truth by rational individuals, then it is by definition, part of truth. Subsequent philosophers such as Whitehead and Russell expounded on the concept of truth. According to these philosophers, there exists a set of truths which in character is both relative and self-sufficient. Truth is relative because the discretion of a group of rational individuals is also relative. It is self-sufficient because its consequence is self-compelling. When presented to different individuals, a truth compels the individual to believe and accept it as true. What is the general consequence of these assumptions of truth? In essence, such assumptions reject the notion of absolute truth. Absolute truth defines an epistemological basis of reality; that is, reality bounded not by the laws of nature, but by the law of necessity. One can refer to this reality as Being, Divine entity, or God. However, absolute truth is not necessarily a definitive clause of a Divine entity. Absolute truth is assumed by some philosophers to be manifested in quintessential entities; entities which are purported to exist in reality. It may be argued that this interpretation of reality may be a personalistic interpretation of ends. In any case, it is possible to prove this assumption. References Descartes, Rene. 1637/1999. Discourse on the Method. London: London Publishing House. Kant, Immanuel. 1786/1926. The Critique of Pure Reason. New York: Macmillan Publishing Company.

The Similarities and Differences between The Raven and Ode to a Nightingale Poems Free Essay Example, 2000 words

The setting of Poe s Raven mirrors the state of physical and emotional isolation of the persona. The literary piece begins at the dead of night in December, which happens to be the last month of the year when one retraces their steps throughout the ending year; when the painful occurrences which were beyond the person in question return to haunt them. As such, December is a month of social and emotional isolation created by thoughts of loved ones who have been lost throughout the year. In addition, the narrator s lone sleeping chamber and his lack of company are also symbolic of loneliness and isolation. The storyteller cuts the image of a weak and troubled man, who appears stuck in his own prison where there is no sign of life around, but his. He hopes morning will come and bring with it the beauty of light and social life, but in the meantime, he has to endure the pains of isolation, more so from his departed Lenore. The ensuing story built around isolation is simple, persistent and tragic. The poem splits the characters and themes into two opposing worlds of dead darkness of isolation; and hope of a reunion by daybreak. We will write a custom essay sample on The Similarities and Differences between The Raven and Ode to a Nightingale Poems or any topic specifically for you Only $17.96 $11.86/page Delighting music even motivates the narrator to welcome his death because he is overwhelmed by the negative impacts of isolation. The song claims the suffering may end in his afterlife. But when, following his meditation, he rediscovers himself and recognizes his real status by uttering the word "forlorn, " the narrator abandons his illusory escape from the unavoidable, and like the narrator in the Raven, he feels unable to chart his destiny in the current state of isolation.