Hydrogen Bond Analysis Service

Hydrogen bonding is a weak force that forms a special type of dipole-dipole attraction, when hydrogen atoms occurs when bonding to another electronegative atom with a lone pair of electrons present in a strongly electronegative atom. These bonds are generally stronger than ordinary dipole-dipole and dispersion forces, but weaker than true covalent bonds and ionic bonds. The hydrogen atom and the electronegativity atom X are covalently bonded. If it is close to the atom with a large electronegativity and a small radius Y (OFN, etc.), the hydrogen between X and Y is used as a medium to generate the XH ... Y form. [X and Y can be the same kind of molecules, such as hydrogen bonds between water molecules; they can also be different kinds of molecules, such as hydrogen bonds between ammonia monohydrate molecules (NH3 · H2O)].

Our simulation services

Project name Hydrogen bond analysis service
Samples requriements The initial structure of PDB ID, etc.
Detection cycle 3-5 days.
Service including We provide you with raw data and calculation result analysis service.
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Calculation of intramolecular hydrogen bonding

Intramolecular hydrogen bonds must have the necessary conditions for forming hydrogen bonds, but they must also have specific conditions, for example: the formation of a planar ring, the most stable size of the ring is a ring with five or six atoms, and no distortion is being formed In the ring.

Calculation of double hydrogen bond and Π hydrogen bond

Different molecules may also form a double hydrogen bond effect, so double hydrogen bonds are also regarded as intermediates for hydride dehydrogenation. In addition, π-hydrogen bonds are often present in large molecules. Large π bonds or delocalized π bond systems have large electron clouds that can be used as proton acceptors and form π-hydrogen bonds (also called aromatic hydrogen bonds). They are stable peptides and proteins also play an important role .

An example on how we analyze hydrogen bonding

Running the CPPTRAJ script will generate the files: avg.dat, hbond.gnu, contacts-lifetime.dat and crv.contacts-lifetime.dat. The avg.dat file will print the average of each solute-solute hydrogen bond (sorted by population) formed over the course of the trajectory. Looking at the first 10 lines of the avg.dat, we have:

Hydrogen bond analysis service

The lifetime analysis allows the study of the time-dependent behavior of the hydrogen bonds. The first 10 lines of the file contacts-lifetime.dat are:

Hydrogen bond analysis service 1

Using the bash command to sort the file using the 5th column (lifetime frames) returns:

Hydrogen bond analysis service 2

Hydrogen bond analysis service 3

ComputaBio provides corresponding molecular dynamics analysis services. Structure and function are the central issues of modern molecular biology. The interaction between molecules is the cornerstone of this axis problem. The interactions between molecules mainly include covalent bonds, ionic bonds, hydrogen bonds, van der Waals forces, hydrophobic interactions, etc. The ComputaBio team has been working in this field for more than ten years, and can provide you with accurate analysis of related forces. If you have needs in this regard, please feel free to contact us.

* It should be noted that our service is only used for research, not for clinical use.


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