The local vibrational mode theory and its place in the vibrational spectroscopy arena

E Kraka, M Quintano, HW La Force… - The Journal of …, 2022 - ACS Publications
This Feature Article starts highlighting some recent experimental and theoretical advances
in the field of IR and Raman spectroscopy, giving a taste of the breadth and dynamics of this …

[HTML][HTML] Quantum mechanical assessment of protein–ligand hydrogen bond strength patterns: insights from semiempirical tight-binding and local vibrational mode …

A Madushanka, RT Moura Jr, N Verma… - International Journal of …, 2023 - mdpi.com
Hydrogen bonds (HB) s are the most abundant motifs in biological systems. They play a key
role in determining protein–ligand binding affinity and selectivity. We designed two …

Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study

JJ Antonio, E Kraka - Biochemistry, 2023 - ACS Publications
Protein dynamics and function is strongly connected to the energy flow taking place.
Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational …

Automatic generation of local vibrational mode parameters: from small to large molecules and QM/MM systems

RT Moura Jr, M Quintano, JJ Antonio… - The Journal of …, 2022 - ACS Publications
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 …

Decoding chemical bonds: assessment of the basis set effect on overlap electron density descriptors and topological properties in comparison to QTAIM

CV Santos Jr, SA Monteiro, ASC Soares… - The Journal of …, 2023 - ACS Publications
Quantum chemical bonding descriptors based on the total and overlap density can provide
valuable information about chemical interactions in different systems. However, these …

Hydrogen Sulfide Ligation in Hemoglobin I of Lucina pectinata─A QM/MM and Local Mode Study

M Freindorf, J Antonio, E Kraka - The Journal of Physical …, 2023 - ACS Publications
In this study, we investigated the interaction between the H2S ligand and the heme pocket of
hemoglobin I (HbI) of Lucina pectinata for the wild-type protein; three known mutations …

Chemical bonding in Uranium‐based materials: A local vibrational mode case study of CsUOCl and UCl crystals

F Bodo, A Erba, E Kraka… - Journal of Computational …, 2024 - Wiley Online Library
Abstract The Local Vibrational Mode Analysis, initially applied to diverse molecular systems,
was extended to periodic systems in 2019. This work introduces an enhanced version of the …

Iron–histidine bonding in bishistidyl hemoproteins–A local vibrational mode study

M Freindorf, JJ Antonio, E Kraka - Journal of Computational …, 2024 - Wiley Online Library
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and
ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and …

[HTML][HTML] Exploring Jahn-Teller distortions: a local vibrational mode perspective

M Quintano, RT Moura Jr, E Kraka - Journal of Molecular Modeling, 2024 - Springer
The characterization of normal mode (CNM) procedure coupled with an adiabatic
connection scheme (ACS) between local and normal vibrational modes, both being a part of …

Local vibrational mode theory meets graph theory: Complete and non-redundant local mode sets

M Quintano, RT Moura Jr, E Kraka - Chemical Physics Letters, 2024 - Elsevier
Abstract This Frontiers Article introduces a unique perspective on the well-established
concept of completeness in a chemically meaningful set of non-redundant local vibrational …