Hydrogen bond | EPFL Graph Search

In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the period 2 elements nitrogen (N), oxygen (O), and fluorine (F). Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent or ionic bon

Stability and physical properties of alkylsilane and alkylphosphonate self-assembled monolayer (SAM) films on metal oxide substrates characterized at the micro- and nanoscale

Enamul Hoque

Self-assembled monolayer (SAM) films have attracted immense attention for both fundamental and applied research. A SAM is composed of a large number of molecules with a head group that chemisorbs onto a substrate, a tail group that interacts with the outer surface of the film, and a spacer (backbone) chain group that connects the head and tail groups resulting in a coating. Interactions between spacer groups of different molecules, such as van der Waals forces and/or hydrogen bonding, hasten SAM film formation and contribute to its stability. In this dissertation, SAM and thin films have been formed onto copper and aluminum oxide surfaces by reaction with 1H,1H,2H,2H-perfluorodecyldimethylchlorosilane (PFMS), 1H,1H,2H,2H-perfluorodecyltrichlorosilane (PFTS), 1H,1H,2H,2H-perfluorodecylphosphonic acid (PFDP), octylphosphonic acid (OP), decylphosphonic acid (DP), and octadecylphosphonic acid (ODP). The properties and stability of the films were investigated employing complementary surface analysis techniques: X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), friction force microscopy (FFM), a derivative of AFM, contact angle measurements (CAMs), and Fourier transform infrared reflection/absorption spectroscopy (FT-IRRAS). The perfluoroalkylsilane SAM on Cu is found to be extremely hydrophobic typically having sessile drop static contact angles of more than 130° for pure water and a surface energy of 14 mJ/m2 (mN/m). FFM showed a significant reduction in the adhesive force and friction coefficient of PFMS modified Cu (PFMS/Cu) compared to unmodified Cu. Treatment by exposure to harsh conditions showed that PFMS/Cu SAM can withstand boiling nitric acid (pH=1.8), boiling water, and warm sodium hydroxide (pH=12, 60 °C) solutions for at least 30 minutes. Furthermore, no SAM degradation was observed when PFMS/Cu was exposed to warm nitric acid solution for up to 70 min at 60 °C or 50 min at 80 °C. XPS and FT-IRRAS data reveal a coordination of the PFMS silicon (Si) atom with a cuprate (CuO) molecule present on the oxidized copper substrate. The data give good evidence that the stability of the SAM film on the PFMS modified oxidized Cu surface is largely due to the formation of a siloxy-copper (-Si-O-Cu-) bond via a condensation reaction between silanol (-Si-OH) and copper hydroxide (CuOH). For a PFTS modified Cu surface (PFTS/Cu), the sessile drop static contact angle of pure water has been measured to be more than 125° and the surface energy to be typically less than 16 mJ/m2. Stability tests show that the PFTS/Cu film can survive in boiling pure water for one hour, boiling nitric acid (pH 1.5 or 1.8) for 30 minutes, sodium hydroxide solution (pH 12, 70 °C) for 30 minutes, and autoclave conditions (steam at 134 °C and 3 atmospheres) for 15 minutes. The more commonly used self-assembled monolayer (SAM) modifications of Cu surfaces, e.g. thiol compounds, are significantly less stable than PFTS/Cu. Extremely hydrophobic (low surface energy) and stable PFMS/Cu SAMs and PFTS/Cu films could be useful as corrosion inhibitors in micro/nanoelectronic devices and/or as promoters for anti-wetting, low adhesion surfaces or drop-wise condensation on heat exchange surfaces. XPS analysis confirmed the presence of perfluorinated and non-perfluorinated alkylphosphonate molecules on the PFDP, DP, and ODP SAMs deposited at the aluminum oxide coated silicon (Al/Si) surfaces. The sessile drop static contact angle of pure water on PFDP SAMs was typically more than 130° and on DP and ODP typically more than 125° indicating that the phosphonic acid SAMs reacted with Al samples were very hydrophobic. The surface roughness for PFDP/Al, DP/Al, ODP/Al, and bare Al was approximately 35 nm, as determined by AFM. The surface energy for PFDP/Al was determined to be approximately 11 mJ/m2 by the Zisman plot method compared to 21 mJ/m2 and 20 mJ/m2 for DP/Al and ODP/Al, respectively. PFDP/Al gave the lowest adhesion and friction force while bare Al gave the highest. The adhesion and friction forces for ODP/Al and DP/Al SAMs were in between. ODP, DP, and OP SAMs have been studied in detail on relatively flat aluminum oxide surfaces. The rms surface roughness for ODP/Al, DP/Al, OP/Al, and bare Al was less than 15 nm, as determined by AFM. The sessile drop static contact angle of pure water on ODP/Al and DP/Al was typically more than 115° and on OP/Al typically less than 105°. The surface energy for ODP/Al and DP/Al was determined to be approximately 21 mJ/m2 and 22 mJ/m2, respectively, compared to 26 mJ/m2 for OP/Al. ODP/Al and OP/Al were studied by FFM to better understand their micro-/nano-tribological properties. ODP/Al gave the lowest coefficient of friction values while bare Al gave the highest. The adhesion forces for ODP/Al and OP/Al were comparable. The chemical stability of ODP/Al, PFDP/Al, DP/Al, OP/Al, and PFMS/Al SAMs has been inspected by exposure to warm nitric acid (pH 1.8, 30 min, 60-95 °C). The XPS data and stability against harsh chemical conditions indicate that a type of bond forms between a phosphonic acid (PA) or silane molecule and the oxidized Al surface. Stability tests using warm nitric acid (pH 1.8, 30 min, 60-95 °C) show ODP/Al SAMs to be most stable followed by PFDP/Al, DP/Al, PFMS/Al, and OP/Al SAMs. For PFTS/Al, stability tests demonstrate that modified aluminum is able to survive exposure to warm nitric acid (pH = 1.8, 60 °C, 30 min) indicating some degree of robustness. Hydrophobic, low adhesion, and robust aluminum surfaces have useful applications for micro/nano-electromechanical systems (MEMS/NEMS), such as digital micro-mirror devices (DMDs). These studies are expected to aid in the design and selection of proper lubricants for MEMS/NEMS.

EPFL2007

[(Methylcarbamothioyl)disulfanyl]methyl N-methylcarbamodithioate

Ghulam Murtaza, Christine Neuhausen

The title compound, C5H10N2S5, was unintentionally obtained as the product of an attempted synthesis of a methyl-carbamodithioic acid using methylamine and carbon disulfide. In the molecule, two dithiocarbamate groups are bridged by a -CH2S- unit. The C-S-S-C torsion angle is -90.13 (11)degrees. The crystal structure is stabilized by N-H center dot center dot center dot S interactions between neighbouring molecules. An intramolecular N-H center dot center dot center dot S hydrogen bond also occurs.

2010

Second harmonic scattering of water in a biological context

Tereza Schönfeldová

Water is one of the most abundant molecules in the universe. It forms a hydrogen bond network with unique structure and dynamics. Hydrogen bonding is highly relevant to many biological processes including membrane formation, protein folding, adsorption, and lubrication. However, the underlying molecular interactions within water and between water and membranes are difficult to study and hence not fully understood. In this thesis, we utilize second harmonic scattering (SHS) to investigate inhomogeneities in bulk water, probe structural changes in lipid bilayer membranes, and detect and characterize protein-membrane interactions. Firstly, we explore the structure of bulk water in comparison to a common model liquid, carbon tetrachloride. Combining SHS measurements and molecular dynamics simulations, we report on the nanoscale inhomogeneities in bulk water that occur on femtosecond timescales. We attribute the rise in the coherent second harmonic (SH) intensity to charge density fluctuations with enhanced nanoscale polarizabilities around transient voids. Even though the transient voids also exist in carbon tetrachloride, they do not show polarizability fluctuations and the SH response of carbon tetrachloride thus corresponds to that of a model isotropic liquid. Then, we study the structure of water around large unilamellar vesicles (LUVs), which serve as a model for cell membranes. We focus on the role of water during the lipid melting phase transition. Using SHS, differential scanning calorimetry, and temperature-dependent zeta-potential measurements, we investigate the structural changes of hydration shells around the vesicle membrane. We use lipids with phosphoserine, phosphocholine, and phosphate headgroups and observe different hydration behavior upon the lipid melting transition depending on the membrane composition. Next, we characterize the interface of membranes composed of lipids containing phosphocholine and phosphate headgroups in solutions with different CaCl2 concentrations. We observe that the SH intensity is decreasing with the addition of CaCl2, which we attribute to the formation of a condensed layer of Na+ counterions on the inner leaflet of the LUVs. Additionally, we extract the vesicle surface potential and second-order surface susceptibility from SHS data for membranes with different content of lipids with phosphate headgroups, and observe composition dependent behaviour which suggests structural membrane reorganization. We continue by exploring protein-membrane interactions using water as a contrast agent. We study a pore-forming toxin, perfringolysin O (PFO), known for selective insertion into cholesterol-rich membranes. Combining SHS measurements and cryo-electron microscopy, we compare the interaction between PFO and LUV membranes with a high and low cholesterol content. By obtaining a sub-picomolar insertion constant of PFO, we show that SHS can be used to determine protein-membrane binding constants in concentration ranges not accessible by conventional methods.Finally, we investigate the interaction of protein aerolysin and its mutants with lipid membranes. We observe changes in surface charge in the cap region of membrane-bound aerolysin at different pH of the surrounding solution. By combining SHS with single-channel measurements, we obtain the membrane binding constant of wild-type aerolysin and its mutants, and we dissect their pore-forming mechanism.