Related papers: Do cooperative cycles of hydrogen bonding exist in…
The cooperative effect plays a significant role in understanding the intermolecular donor-acceptor interactions of hydrogen bonds (H-bonds, D-H...A). Herein, using the benchmark method of high-precision ab initio, the well-known cooperative…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
Fluids under extreme confinement exhibit unique structures and intermolecular bonding, distinct from their bulk analogs, driving innovative applications at the water-energy nexus. Probing confined water experimentally at the length scale of…
Hydrogen bonding plays a role in the microphase separation behavior of many block copolymers, such as those used in lithography, where the stronger interactions due to H-bonding can lead to a smaller period for the self-assembled…
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…
Through density functional theory and molecular dynamics calculations, we have analysed various metal polyhydrides to understand whether hydrogen is present in its molecular or atomic form - tetrahydrides of Ba,Sr,Ra, Cs and La;…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We applied coherence analysis to molecular dynamics simulations of the plant protein crambin, a thionin storage protein found in Abyssinian cabbage. Coherence analysis was developed by engineers to identify linear interactions, without…
Hydrogen bonds (HBs) play an important role in the rotational dynamics of organic cations in hybrid organic/inorganic halide perovskites, affecting the structural and electronic properties of the perovskites. However, the properties and…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) or lysozyme with linear…
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
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…
The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…