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Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across…
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
Hydrogen-bond networks govern molecular structure and function across chemistry, biology and materials science, yet their deterministic control at the atomic scale remains a central challenge (1-9).Here, we directly visualize how an…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
Quantum mechanical tunneling of atoms is increasingly found to play an important role in many chemical transformations. Experimentally, atom-tunneling can be indirectly detected by temperature-independent rate constants at low temperature…
We employ Molecular Dynamics (MD) and Time-Dependent Density Functional Theory (TDDFT) to explore the fluorescence of Hydrogen-bonded dimer and trimer structures of Cyclic FF (Phe- Phe) molecules. We show that in some of these…
We expand the definition of our recently proposed proton conduction mechanism, the packed-acid mechanism, which occurs under conditions of concentrated proton donors. The original definition stated that acid-acid interactions, which help…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
Quantum tunneling reactions play a significant role in chemistry when classical pathways are energetically forbidden, be it in gas phase reactions, surface diffusion, or liquid phase chemistry. In general, such tunneling reactions are…
Under cold compression, hydrogen bonding was considered to dominate intermolecular interaction during the ionization of ammonia. Here, we provide experimental and theoretical evidence of intermolecular HH coupling in dense ammonia. Ab…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The closure of cooperative chains of Hydrogen Bonding, HB, to form cycles can enhance cooperativity. Cycles of charge transfer can balance charge into and out of every site, eliminating the charge build-up that limits the cooperativity of…
The low degradability of common polymers composed of light elements, results in a serious impact on the environment, which has become an urgent problem to be solved. As the reverse process of monomer polymerization, what deviates…
Benzoic acid (BA) is a model system for studying proton transfer (PT) reactions. The properties of solid BA subject to high pressure (exceeding 1 kbar = 0.1 GPa) are of particular interest due to the possibility of compression-tuning of the…
The quantum motions of hydrogen (H) atoms play an important role in the dynamical properties and functionalities of condensed phase materials as well as biological systems. In this work, based on the transfer matrix method and…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
A first-principles coupled electron-nuclear dynamics simulation based on real-time, time-dependent density functional theory and Ehrenfest dynamics quantitatively repro-duces bimodal translational energy loss and angular distributions…