Manual of LModeA-nano
This manual focuses on the LModeA-nano as a PyMOL plugin designed to perform Local Vibrational Mode Analysis on both solids and molecules. This theoretical tool can quantify the intrinsic strength of chemical bonds in terms of local stretching force constant.
Since the publication of LModeA-nano in 2022, it has been trusted and applied by many scientists in their research published in Nature, J. Am. Chem. Soc., Chem. Sci., Angew. Chem. Int. Ed., Sci. Adv. and other internationally recognized journals.
Recent news and publications
[2026-02-06] LModeA-nano was employed by Prof. Yang Wang’s research group to extract bond force constants through local vibrational mode analysis of Hessian matrices derived from fixed-bond-length first-principles calculations, enabling quantitative evaluation of temperature-induced bond stiffness variations in their work titled Extending the Elastic Modulus Prediction Model for Covalently Bonded Materials towards the Application in Different Temperatures published in Model. Simul. Mater. Sci. Eng.
[2026-01-23] LModeA-nano was employed by Prof. Yuanyuan Li and Prof. Dingfeng Yang’s research groups to perform local vibrational mode analysis and quantify bond stiffness variations underlying thermal expansion behavior in their work titled Local Bond Engineering in LiMBO₄ (M = Si, Ge): Synergistic Negative Grüneisen Parameter and Bond Stiffening for Reduced Thermal Expansion published in Chem. Mater.
[2025-12-01] LModeA-nano was used by Prof. Adam A. L. Michalchuk’s research group to obtain local mode force constants through an automated analysis of dynamical matrices derived from Γ-point phonon calculations, which served as a benchmark to investigate how computational parameters—specifically the charge density grid—affect the description of chemical bonding strengths in organic molecular crystals in their work titled Converging ab initio Phonon Simulations for Organic Molecular Crystals: the Effect of Charge Density Grids and Phonon Dispersion Sampling published in CrystEngComm.
[2025-11-18] LModeA-nano was used by Prof. Norman Lu and Prof. Joseph S. Francisco’s research groups to calculate the local mode force constants of the methylene C–H bonds in three fluorinated zinc complexes (I–III), which allowed them to verify that the intrinsic strength of these C–H bonds follows a linear correlation with their neutron diffraction bond lengths (Badger’s rule) and to confirm that the blue-shifting C–H⋯F hydrogen bonds are covalent in nature based on the Cremer-Kraka criterion (force constants > 3 mdyn/Å) in their work titled Neutron Diffraction and Spectroscopic Studies of Intramolecular Tetrel Bonds in Three Fluorinated Zinc Complexes: Significant Redshift in the sp3 C−H Stretch Confirmed by Experiments and Theory published in J. Am. Chem. Soc.
[2025-11-10] LModeA-nano was used by Prof. Peter W. Roesky’s research group to quantitatively evaluate the bond strengths within the novel mixed group 14/15 metallacycles—specifically to confirm double-bond character in certain Mo–P and Si–P bonds and to characterize the strength of As–As and Sb–Sb single bonds relative to standard reference molecules in their work titled Pure Molecular Inorganic Rings: Mixed Group 14/15 Metallacycles published in Angew. Chem. Int. Ed.
[2025-09-18] LModeA-nano was used by Prof. Yuanyuan Li and Prof. Dingfeng Yang’s research groups to quantify the local vibrational frequencies and bond strengths of Nb–O and B–O bonds demonstrating that the relatively softer and more anharmonic Nb–O bonds serve as the main source of negative Grüneisen contributions, while the much stiffer B–O bonds provide a rigid structural framework, and the compensation between these two contrasting vibrational behaviors ultimately leads to the low thermal expansion observed in NbBO₄ in their work titled Low Thermal Expansion in Niobate Borate NbBO₄ Enabled by Compensated Grüneisen Parameters of NbO₈ Polyhedra published in Inorg. Chem.
[2025-08-28] LModeA-nano was used by Prof. Haoran Wang’s research group to determine the force constants of the C=C double bond in two different transition states and to help conclude that the bond-stretching energy was not the primary reason for a high energy barrier in one of the reaction pathways in their work titled Inhibition Mechanism of Quercetin on Coal Low-Temperature Oxidation: Molecular Flexibility and Double Bond-Mediated Free Radical Scavenging published on Fuel.
[2025-07-30] LModeA-nano was employed by Prof. Xuaifei Sun and Prof. Peter W. Roesky’s research groups to determine local stretching force constants to assess the bond strength of the Ag-Ag, Au-Au, and Ag-Au bonds in the synthesized bimetallic complexes confirming that these interactions were weak when compared to strong single metal-metal bonds in diatomic molecules in their work titled On-demand Switching from Mono-Silylene to Bis-Silylene to Access mono-, di- and Mixed Coinage Metal Complexes published on Chem. Sci.
[2025-07-25] LModeA-nano was utilized by Prof. Boon K. Teo and Prof. Zhigang Wang’s research groups to assess the effect of an embedded hydrogen atom on the strength of Au-Au bonds in an Au₂₀ cluster, finding that the local vibrational mode force constants for these bonds were uniformly greater in H@Au₂₀ compared to the undoped Au₂₀ in their work titled Parity-Forbidden Superatomic Molecular Orbital Interaction and Aurophilicity Induced H─Au Bonding in H@Au₂₀ published on Sci. Adv.
[2025-04-16] LModeA-nano was employed by Prof. Artur Mardyukov and Prof. Peter R. Schreiner’s research groups to better understand N₆’s structure and gauge where its bonds are likely to break, thereby exploring its intrinsic stability in their work titled Preparation of A Neutral Nitrogen Allotrope Hexanitrogen C2h-N₆ published on Nature.
[2025-02-04] LModeA-nano was utilized by Prof. Zu-Wei Yin, Prof. Luyi Yang and Prof. Feng Pan’s research groups to determine the thermal decomposition path of the CMC binder by identifying bonds with lower strength that are more likely to break first during thermal treatment in their work titled Tailoring Sodium Carboxymethylcellulose Binders for High-Voltage LiCoO₂ via Thermal Pulse Sintering published on Angew. Chem. Int. Ed.
[2024-12-04] LModeA-nano was utilized by Prof. Zsolt Kelemen’s research group to quantify the plasticity of the metal-metal bonds in their work titled Deciphering the Direct Heterometallic Interaction in κ³-bis(donor)ferrocenyl-transition-metal Complexes published on Dalton Trans.
[2024-08-05] LModeA-nano was utilized by Prof. Jiong Yang and Prof. Lili Xi’s researh group to explain the defect formation energies in half-Heusler (HH) compounds ABX with A-B chemical bond strength in their work titled The A-Ni Chemical Bond in AᴵᴵᴵNiSb (Aᴵᴵᴵ=Sc, Y, Er) half-Heusler Materials Triggers the Formation of Anomalous Vacancy Defects published on Mater. Today Phys.
[2024-05-03] LModeA-nano was utilized by Prof. Artem A. Mikhailov and Prof. Dominik Schaniel’s research group to characterize the chemical bond strength differences in different photoinduced linkage isomers of K₂[RuCl₅NO] crystal in their work titled Local Force Constants and Charges of the Nitrosyl Ligand in Photoinduced NO Linkage Isomers in A Prototypical Ruthenium Nitrosyl Complex published on Phys. Chem. Chem. Phys.
[2024-04-08] LModeA-nano was utilized by Prof. Biprajit Sarkar, Prof. Peter Vöhringer and Prof. Vera Krewald’s research group to calculate local Na–Nb bond stretching frequency to help estimate the rate constant of N₂ release in their work titled Ultrafast Photogeneration of A Metal–Organic Nitrene from 1,1’-diazidoferrocene published on Chem. Sci.
[2024-02-06] LModeA-nano was utilized by Prof. Ling Chen and Prof. Weidong He’s research group to derive the pyrolysis mechanism of BTA compound by inspecting the chemical bond strength in their work titled Insights Into the 5,5’-bis(1H-tetrazolyl)amine Monohydrate (BTA∙H₂O) Pyrolysis Mechanism: Integrated Experimental and Kinetic Model Analysis published on New J. Chem.
[2024-02-03] LModeA-nano was utilized by Prof. Hans Lischka and Prof. Francisco B. C. Machado’s research group to study the substituent effect in benzene derivatives in their work titled A Multi-Descriptor Analysis of Substituent Effects on the Structure and Aromaticity of Benzene Derivatives: π-Conjugation versus Charge Effects published on J. Comput. Chem.
[2024-01-10] LModeA-nano was utilized by Prof. Ilya V. Chepkasov’s research group to explain the impact of n- and p-type impurities on the mechanical characteristics of PbTe thermoelectric materials using local stretching force constants in their work titled Origin of Brittle Behavior of Doped PbTe-based Thermoelectric Materials published on Appl. Phys. Lett.
[2023-11-29] LModeA-nano was utilized by Prof. Jason B. Love and Prof. Carole A. Morrison’s research group to explain why certain ligands are able to recover rhodium from iridium by calculating the Rh-X bond strength in their work titled Separation of Rhodium from Iridium Through Synergistic Solvent Extraction published on Sep. Purif. Technol.
[2023-10-23] LModeA-nano was utilized by Prof. Cam-Tu Phan Dang’s group to measure the N∙∙∙Z interactions (Z = Si, P, S, Cl) strength in terms of local stretching constant in their work titled Revisiting Conventional Noncovalent Interactions towards A Complete Understanding: From Tetrel to Pnicogen, Chalcogen, and Halogen Bond published on RSC Adv.
[2023-09-14] LModeA-nano was utilized by Prof. Dong Wang’s group to explain difference in mechanical stiffness among GeAs, InSe, CuInTe₂ and PbTe solids based on chemical bond strength in their work titled Anisotropic Ductility and Thermoelectricity of van der Waals GeAs published on Phys. Chem. Chem. Phys.
[2023-04-16] LModeA-nano was utilized by Prof. Weidong He’s research group to derive the possible thermal decomposition mechanism of TATOT compound based on chemical bond strength in their work titled Thermal Behaviors, Thermal Decomposition Mechanism, Kinetic Model Analysis and Thermal Hazard Prediction of 3,6,7-triamino-7H-[1,2,4]triazolo[4,3-b][1,2,4]triazole (TATOT) published on Thermochim. Acta.
[2022-12-22] LModeA-nano was utilized by Prof. Jürgen Evers’s research group to characterize Pd-N bond strength in the newly discovered PdCl(NO) compound in their work titled PdCl(NO) – An Iconic Compound with Corrugated Pd₄Cl₄ Octagons Built Up by Pd₂Cl₂(NO)₂ Moieties published on Z. Anorg. Allg. Chem.
[2022-09-26] LModeA-nano was employed by Prof. Peter W. Roesky’s research group to investigate the existence of Si-Si bonding within silylene compounds in their work titled Stimuli Responsive Silylene: Electromerism Induced Reversible Switching Between Mono- and Bis-Silylene published on Angew. Chem. Int. Ed.
[2021-12-20] Our work titled Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture was published on J. Chem. Theory Comput.
Getting Started
Guides
References
Acknowledgement & Funding
The LModeA-nano project is sponsored by National Science Foundation (CHE 2102461).