LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis

Abstract

The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0−3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is crossplatform, open-source and freely available on GitHub: https://github.com/smutao/ LModeA-nano.

PdCl(NO) – an iconic compound with corrugated Pd4Cl4 octagons built up by Pd2Cl2(NO)2 moieties

“…[26] The strength of the PdÀ N bond is more difficult to estimate by means of vibrational spectroscopy due to a lack of suitable data. By means of a local force constant analysis using the program lmodeA-nano [27] the value for the PdÀ N force constant is determined to be in the range around 206 N m À 1 . [28] This size is attributed to predominantly covalent forces similar to the situation of the Pd bond in PdÀ CO, PdÀ SiO or PdÀ NO (precise values obtained by normal coordinate analyses: f(PdÀ C) = 285, f(PdÀ Si) = 245, [29] f(PdÀ N) = 315 N m À 1 [21] ).…”

Shedding Light on the Vibrational Signatures in Halogen‐Bonded Graphitic Carbon Nitride Building Blocks

“…[65] Pertinent results for the XB monomers and dimer complexes are reported in the % contribution tables found in the Supporting Information. Local vibrational theory is discussed extensively in the recent literature by Kraka et al [63,66,67]…”

On the nature of inter-anion coinage bonds

“…22 Hence, the energy difference between the local minimum and TS (well-depth) serves as an energy measurement for the metastability. Alternatively, the local bond stretching force constant, [102][103][104][105] which is an ''in situ'' descriptor for the strength of a specified chemical bond, [106][107][108][109][110][111][112] has been utilized to describe the inter-anion hydrogen bonds. 113 Criteria for the inter-anion phenomena have also been developed based on the QTAIM approach, 68,69 which has been broadly applied to from the interpretations of novel chemical bonding 114 to the developments of QM-based force fields for large-scale molecular simulations.…”

“…In addition, the inter-anion CiBs found in crystal structures 14,100,101 were inspected in vacuum and condensed phase by employing the solvation model based on density (SMD). 163 Subsequently, the metastability was further examined using the QTAIM method, 68,69 the local vibrational mode theory, 104,105,[164][165][166] and the ab initio molecular dynamics (AIMD) simulations. At last, key factors for the kinetic stability were elucidated by employing the BLW-ED approach.…”