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Related Concept Videos

Physical Properties of Amines01:26

Physical Properties of Amines

Amines with low molecular weight are usually gaseous at room temperature, while those with high molecular weight are liquid or solids in nature. Usually, low molecular weight amines have a rotten fish-like smell. Diamines typically have a pungent smell. For instance, cadaverine and putrescine, depicted in Figure 1, are two molecules responsible for decaying tissue.
Preparation of 1° Amines: Gabriel Synthesis01:28

Preparation of 1° Amines: Gabriel Synthesis

Direct alkylation is not a suitable method for synthesizing amines because it produces polyalkylated products. Gabriel synthesis is the most preferred method to exclusively make primary amines. The method uses phthalimide, which contains a protected form of nitrogen that participates in alkylation only once to predominantly give primary amines.
Strong bases like NaOH or KOH deprotonate the phthalimide to form the corresponding anion, which acts as a nucleophile. Further, the anion attacks an...
NMR Spectroscopy Of Amines01:19

NMR Spectroscopy Of Amines

In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is broad and...
Structure of Amines01:19

Structure of Amines

The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...
Basicity of Aliphatic Amines01:21

Basicity of Aliphatic Amines

Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates higher...
Basicity of Heterocyclic Aromatic Amines01:25

Basicity of Heterocyclic Aromatic Amines

Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).

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Related Experiment Video

Updated: Jun 16, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
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An improved generalized AMBER force field (GAFF) for urea.

Gül Altinbaş Ozpinar1, Wolfgang Peukert, Timothy Clark

  • 1Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052, Erlangen, Germany.

Journal of Molecular Modeling
|February 18, 2010
PubMed
Summary
This summary is machine-generated.

Researchers developed an improved generalized AMBER force field (GAFF) parameter set for urea. This enhanced force field accurately predicts urea dimer interactions, aligning with experimental data.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Physical Chemistry

Background:

  • Accurate molecular modeling requires precise force field parameters.
  • Urea's hydrogen bonding capabilities necessitate detailed parameterization for simulations.
  • Existing force fields may not fully capture urea's complex interactions.

Purpose of the Study:

  • To develop an improved force field parameter set for urea within the generalized AMBER force field (GAFF) framework.
  • To enhance the accuracy of molecular simulations involving urea.
  • To provide reliable parameters for studying urea's structural and energetic properties.

Main Methods:

  • Utilized quantum chemical computations, including density functional theory (DFT) and ab initio methods (MP2, CCSD).
  • Employed various basis sets (e.g., 6-311++G(d,p), aug-cc-pVDZ) and complete basis set (CBS) methods.
  • Calculated atomic partial charges using the restrained electrostatic potential (RESP) fitting approach.

Main Results:

  • Generated a new GAFF parameter set for urea, incorporating optimized geometrical and energetic parameters.
  • Validated interaction energies against high-level correlated calculations (CCSD, MP2).
  • Achieved good agreement between force field calculations and experimental data for urea dimer structures.

Conclusions:

  • The developed GAFF parameter set offers improved accuracy for simulating urea.
  • The new parameters enhance the reliability of molecular dynamics and other simulations involving urea.
  • This work contributes to more precise computational studies of systems containing urea.