Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems

Abstract

LModeAGen, a new protocol for the automatic determination of a nonredundant, complete set of local vibrational modes is reported, which is based on chemical graph concepts. Whereas local mode properties can be calculated for a selection of parameters targeting specific local modes of interest, a complete set of nonredundant local mode parameters is requested for the adiabatic connection scheme (ACS), relating each local vibrational mode with a normal mode counterpart, and for the decomposition of normal modes (CNM) in terms of local mode contributions, a unique way to analyze vibrational spectra. So far, nonredundant parameter sets have been generated manually following chemical intuition or from a set of redundant parameters in a trial-and-error fashion, which has hampered the study of larger systems with hundreds of parameters. LModeAGen was successfully applied for a test set of 11 systems, ranging from small molecules to the large QM (>100 atoms) subsystem of carbomonoxy-neuroglobin protein, described with a hybrid QM/MM method. The ωB97X-D/aug-cc-pVDZ, M06L/def2-TZVP, and QM/MM ωB97X-D/6-31G(d,p)/AMBER model chemistries were adopted for the description of the molecules in the test set. Our new protocol is an important step forward for a routine ACS and CNM analysis of the vibrational spectra of complex and large systems with hundreds of atoms, providing new access to important encoded electronic structure information.

Quantum Mechanical Assessment of Protein–Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory

“…[ 133 ], and hydrogen bonds [ 30 , 134 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 142 ]. Recently, the quantitative assessment of bond strength in biological systems applying a QM/MM methodology [ 143 , 144 , 145 ] and the analysis of bonding in actinide and lanthanide compounds have been added to the LMA repertoire [ 146 , 147 , 148 ]. LMA also successfully revised a number of concepts, such as the characterization of metal-ligand interactions, replacing the Tolman electronic parameter (TEP) with the more accurate metal-ligand electronic parameter (MELP), based on local mode force constants [ 149 , 150 , 151 , 152 , 153 ].…”

MQM 2022: The 10th Triennial Conference on Molecular Quantum Mechanics

“…They examine the convergence behavior of the algorithm for properties such as NMR shielding constants and excitation energies. Then, Moura and co-workers from the Kraka group at Southern Methodist University outline a new protocol called “LModeAGen” for the determination and analysis of local vibrational modes . This approach avoids chemical intuition in the creation of nonredundant parameter sets and thus provides a unique method to studying larger molecular systems.…”

Decoding Chemical Bonds: Assessment of the Basis Set Effect on Overlap Electron Density Descriptors and Topological Properties in Comparison to QTAIM

“…Additionally, the local vibrational mode (LVM) theory 23−25 developed by Konkoli and Cremer 26 is a powerful tool for deriving chemical bond local mode properties from normal vibrational modes. LVM analysis has led to a new way of analyzing vibrational spectra, as shown in recent applications such as the investigation of pK a probes, 27 to gain insights into vibrational Stark effect probes, 28 the analysis of characteristic vibrational coupling in nucleobases and Watson−Crick base pairs of DNA, 29 bond strength in biological systems through quantum-mechanics/molecular-mechanics (QM/MM), 25,30,31 the assessment of underlying properties of lanthanide compounds, 32 and the recent evaluation of protein−ligand hydrogen bond strength patterns. 33 The overlap property (OP) model, introduced by Malta and colleagues, 34 is a set of chemical bonding descriptors that has recently been extended.…”

“…Among the various chemical bond models available, the quantum theory of atoms in molecules (QTAIM), energy decomposition analysis (EDA), − electron localized function (ELF), and natural bond orbitals (NBOs) are widely used. Additionally, the local vibrational mode (LVM) theory − developed by Konkoli and Cremer is a powerful tool for deriving chemical bond local mode properties from normal vibrational modes. LVM analysis has led to a new way of analyzing vibrational spectra, as shown in recent applications such as the investigation of p K a probes, to gain insights into vibrational Stark effect probes, the analysis of characteristic vibrational coupling in nucleobases and Watson–Crick base pairs of DNA, bond strength in biological systems through quantum-mechanics/molecular-mechanics (QM/MM), ,, the assessment of underlying properties of lanthanide compounds, and the recent evaluation of protein–ligand hydrogen bond strength patterns …”

“…However, it has since been successfully applied to a range of systems, including diatomics, molecular, coordination compounds, and solid-state materials. − Understanding the overlap polarizability is key to understanding the relationship between 4f–4f transition intensities and the Ln–L covalent character. − The OP model has also been expanded to calculate overlap properties in polyatomic molecules through localized molecular orbitals, such as the Pipek–Mezey localization method, which can be done using various atomic charge partitioning methods, including Mulliken, Löwdin, Hirshfeld, Bader, and Becke populations . Moreover, the OP approach has been applied to describe chemical bonding in organic reaction systems, yielding results in excellent agreement with other chemical bonding analysis models, such as QTAIM and LVM. − …”