Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Introduction to Chemical Bonds01:01

Introduction to Chemical Bonds

13.6K
Chemical Bonds
The electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms. The innermost electron shell has a maximum capacity of two electrons, but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states that, with the exception of the innermost shell, atoms are most stable energetically when they have eight electrons in their valence shell, the...
13.6K
Molecular Shapes01:18

Molecular Shapes

63.3K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
63.3K
Bond Polarity, Dipole Moment, and Percent Ionic Character02:48

Bond Polarity, Dipole Moment, and Percent Ionic Character

36.7K
Bond Polarity
36.7K
Cohesion01:07

Cohesion

60.4K
Cohesion is the attraction between molecules of the same type, such as water molecules. Water molecules have an overall neutral charge but are polar molecule. An oxygen atom in one water molecule has a partial negative charge that can bind to a hydrogen atom with a partial positive charge in a second water molecule, forming a hydrogen bond. Each water molecule can form up to four hydrogen bonds with other water molecules. Hydrogen bonds are responsible for water's cohesive nature.
On a...
60.4K
Newman Projections02:06

Newman Projections

24.1K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
24.1K
IR Spectrum Peak Broadening: Hydrogen Bonding01:23

IR Spectrum Peak Broadening: Hydrogen Bonding

2.2K
The vibrational frequency of a bond is directly proportional to its bond strength. As a result, stronger bonds vibrate at higher frequencies, while weaker bonds vibrate at lower frequencies. The stretching vibration of the strong O–H bond in alcohols and phenols (very dilute solution or gas phase) appears as a sharp peak at 3600–3650 cm−1.
However, the extent of hydrogen bonding influences the observed stretching frequency and band broadening. Intermolecular or intramolecular...
2.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Suppressing Interfacial-Accelerated Degradation in Perovskite Solar Cells via Supramolecular Co-Assembly.

Angewandte Chemie (International ed. in English)·2026
Same author

Thermal-decoupled selenization enables kesterite solar cells with 15.3% certified efficiency.

Nature communications·2026
Same author

Lithio-Gel via Lithium Bonding: Mitigating Anode Failure by Blocking Crosstalk in Rechargeable Li-SOCl<sub>2</sub> Batteries.

Journal of the American Chemical Society·2026
Same author

Intramolecular Design of Poly(ethylene oxide) for Solid-State Electrolytes and Next-Generation High-Energy Batteries.

Nano-micro letters·2026
Same author

Hydrogen-Bond-Networked Robust Binder Enabling Long-Cycling Sulfide-Based All-Solid-State Lithium Batteries.

Angewandte Chemie (International ed. in English)·2026
Same author

Revised Solvent Rule Unlocks Non-Conventional Solvents for Na<sup>+</sup>-Solvent Co-Intercalation in Graphite.

Advanced materials (Deerfield Beach, Fla.)·2026

Related Experiment Video

Updated: Mar 29, 2026

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy
10:28

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

Published on: May 27, 2018

9.6K

SPAM: A Simple Approach for Profiling Bound Water Molecules.

Guanglei Cui1, Jason M Swails2, Eric S Manas1

  • 1Computational Chemistry US, Platform Technology and Sciences, GlaxoSmithKline Pharmaceuticals , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.

Journal of Chemical Theory and Computation
|November 24, 2015
PubMed
Summary

A new method, SPAM (Site-specific Protein hydration Analysis Method), analyzes protein hydration shells and water molecule free energies using molecular dynamics simulations. This approach aids in understanding binding interactions and drug discovery.

More Related Videos

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.8K
In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS
09:48

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

Published on: February 15, 2016

8.9K

Related Experiment Videos

Last Updated: Mar 29, 2026

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy
10:28

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

Published on: May 27, 2018

9.6K
Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.8K
In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS
09:48

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

Published on: February 15, 2016

8.9K

Area of Science:

  • Computational chemistry
  • Structural biology
  • Biophysics

Background:

  • Water molecules play a crucial role in protein structure and function.
  • Understanding the hydration shell is key to deciphering protein-ligand interactions.
  • Accurate estimation of water molecule free energies is challenging.

Purpose of the Study:

  • To introduce a novel computational method, SPAM (Site-specific Protein hydration Analysis Method), for analyzing protein hydration shells.
  • To estimate the relative free energies of water molecules within the hydration shell.
  • To provide a tool for prospective application in drug discovery.

Main Methods:

  • Utilizes explicit solvent molecular dynamics (MD) simulations.
  • Identifies discrete hydration sites at the water-protein interface.
  • Computes local free energy measures from interaction energy distributions.

Main Results:

  • SPAM successfully captures hydration shell structure and estimates water molecule free energies.
  • The method provides a qualitative thermodynamic profile of bound water molecules.
  • Results correlate well with established structure-activity relationships and binding hot spots.

Conclusions:

  • SPAM offers a simple yet effective approach to analyze protein hydration.
  • The method demonstrates utility in retrospective analyses of known protein systems (HIV1 protease, lysozyme).
  • SPAM has potential for prospective application in drug discovery processes.