Ambit-HNMR: an open source tool for prediction of 1H-NMR chemical shifts

We present a new software tool, Ambit-HNMR, for automatic calculation of ¹H-NMR chemical shifts of organic compounds. Ambit-HNMR is an open-source software, written in Java, part of the chemoinformatics platform Ambit. Ambit-HNMR software uses a CDK based molecule presentation as connection table where H atoms are treated implicitly. The chemical shifts for each H atom are calculated by means of so called H-atom environments which describe different types of resonance protons. Each H-atom environment consists of: (1) a SMARTS pattern defining a molecular substructure; (2) base H shift, Z₀; (3) atom positions {a₁, a₂, …, a_n} and distances within the substructure; (4) a set of possible substituents {S₁, S₂, …, S_k} described by SMARTS patterns and (5) associated chemical shifts, {Z_i1, Z_i2, …, Z_in}, for each substituent, S_i, respectively for all atoms’ positions of the H-atom environment (i=1, 2, …, k). For an input target structure, all H-atom environments and all substituents, {S_r1, S_r2, … S_rn,}, attached to the corresponding environment positions are identified by means of substructure searching. The chemical shifts for given H atom are calculated by means of additive scheme: Z₀ + Z_r,1 + Z _r,2+ +⋯+Z_rn,n. We have created a knowledge base with H-atom environments for the main classes of organic compounds based on the additive schemes of Pretsch. Additionally, Ambit-HNMR calculates the spin splitting for each chemical shift using the information of the molecule classes of equivalent atoms.

Quick start: write in the console

java -jar ambit-hnmr.jar -s CCC=C

Using default HNMR database: ./hnmr-knowledgebase.txt
Input smiles: CCC=C
1.06 H3 atom 1 multiplicity 3  ALKANES/CH3 0.86 + 0.0 (alpha, -C_alkyl) + 0.2 (beta, -C=C)
2 H2 atom 2 multiplicity 4x2  ALKANES/CH2 1.37 + 0.0 (alpha, -C_alkyl) + 0.63 (alpha, -C=C) + 0.0 (beta, -C=C)
5.03 H2 atom 4 multiplicity 2  ALKENES 5.25 + -0.22 (cis, -C_alkyl)
4.97 H2 atom 4 multiplicity 2  ALKENES 5.25 + -0.28 (trans, -C_alkyl)
5.7 H1 atom 3 multiplicity 3x3  ALKENES 5.25 + 0.45 (gem, -C_alkyl)