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The Theoretical Chemistry Symposium (TCS) series has continued to provide an exciting platform for presenting, sharing, and exchanging emergent ideas on wide ranging topics in Theoretical and Computational Chemistry since its inception in 1986. Following the success of the latest edition, ChemPhysChem has joined hands with two of the main organizers of the symposium (below) to present a Special Collection with contributions from the TCS 2021 participants.

Ashwani Tiwari

Neelanjana Sengupta
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Table of Contents
Efficient Interrogation of the Kinetic Barriers Demarcating Catalytic States of a Tyrosine Kinase with Optimal Physical Descriptors and Mixture Models
- First Published: 16 November 2022

Efficiently quantifying kinetic barriers: Estimation of activation energies related to rare catalytic activity transitions of Tyrosine Kinases is challenged by high computational expense and obscurity of optimal system descriptors. Here, an upgraded expectation maximized molecular dynamics formalism is used to estimate transition barriers, which is more efficient than optimal collective-variables derived with experimental insights.
Oxygen-Induced Dissociation of a Single Water Molecule in Confined 2-D Layers: A Semiempirical Study
- First Published: 15 June 2022

Water dissociation on an oxygen-functionalized h-BN monolayer with and without the graphene layer is investigated using semiempirical calculations. Placing a graphene layer above the h-BN monolayer and continuously tuning the interlayer separation modulates the reaction barrier for the oxygen-induced water dissociation at the bridge site of the h-BN layer, which consequently controls the water-splitting reaction on the free-standing monolayer.
Molecular Electrides: An In Silico Perspective
- First Published: 27 July 2022

Current status of molecular electrides: Using relevant examples, the required characteristics to qualify as an electride, such as non-nuclear attractor, Laplacian of electron density (∇2(ρ(r)), non-linear optical properties, electron localization function, and non-covalent interactions are analyzed.
Dynamical and Mechanical Insights into the Li(2S)+ HCl(
) Reaction: A Detailed Quantum Wavepacket Study
- First Published: 07 November 2022
Assessing the Effect of Dopants on the C−H Activation Activity of γ-Al2O3 using First-Principles Calculations
- First Published: 02 November 2022

The influence of neighbouring metal dopants (boron and gallium) in altering the catalytic activity of γ-Al2O3 is demonstrated using density functional calculations. Gallium greatly improves the catalytic activity of the material. A correlation between H2 binding energies and the C−H activation free energies is identified.
Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study
- First Published: 31 October 2022

Molecular dynamics simulations were performed for the translocation of polyelectrolytes (PE) through a nanopore, which elucidated a synergistic coupling between the salt-concentration-induced screening effect and the drift force originating from the salt-concentration gradient, thus affecting the translocation time.
Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations
- First Published: 17 November 2022
Acetylene-Mediated Borophosphene Dirac Materials as Efficient Anode Materials for Lithium-Ion Batteries
- First Published: 11 March 2023
Photoionization Bands of Cyanogen: Multi-Mode Vibronic Coupling and Renner-Teller Effects
- First Published: 27 February 2023

Vibronic coupling in the first four electronic states of symmetric linear Cyanogen radical cation is studied. Effect of Renner-Teller coupling of electronic states on the vibronic band structure, nonradiative decay and and radiative emission of these four electronic states are examined at length. The electronic potential energy surfaces and their coupling surfaces calculated with the aid of ab initio quantum chemistry methods and first principles nuclear dynamics calculations are carried out on the coupled manifold of electronic states.
E−Z Isomerization in Guanidine: Second-order Saddle Dynamics, Non-statisticality, and Time-frequency Analysis
- First Published: 07 October 2022

The classical dynamics study of the E−Z isomerization reaction of guanidine shows that 15 % of the trajectories follow the second-order saddle pathway. The dynamics was found to be highly non-statistical. Following the dynamics in the frequency ratio spaces reveal the existence of resonance junctions and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior.
A Synergistic Approach towards Optimization of Coupled Cluster Amplitudes by Exploiting Dynamical Hierarchy
- First Published: 31 October 2022

A Synergistic inter-relationship among various cluster amplitudes during Coupled Cluster optimization procedure has been analytically established based on an implicit temporal hierarchy. With significant reduction in the number of independent parameters and memory requirement, the methodology is shown to be nearly as accurate as canonical coupled cluster.
Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe2+/Fe3+ Redox Reaction
- First Published: 28 September 2022

Noise stabilized molecular dynamics together with screened localized orbitals allow achieving a significant speed up in molecular dynamics (MD) simulations. The authors demonstrate the application of this approach in studying the redox properties of the aqueous Fe2+/Fe3+ system by carrying out long MD simulations.
Recent Advances in the Study of Negative-Ion Resonances Using Multiconfigurational Propagator and a Complex Absorbing Potential
- First Published: 12 October 2022
Electronic Substitution Effect on the Ground and Excited State Properties of Indole Chromophore: A Computational Study
- First Published: 05 November 2022

Electronic substitution effects on the excited state properties of indole and its derivatives – tryptophan, serotonin and melatonin are studied using time dependent density functional calculations. The contribution of the small in-plane adjacent groups increases the electron density of the indole ring whereas the out-of-plane long substituent groups have minor effects.
Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding
- First Published: 06 October 2022

Coflin-1 membrane interaction: Coarse-grain simulations are used to investigate the binding of cofilin-1 to phosphoinositide-lipid-containing membranes. The authors show that PIP2 and PIP3 lipids are the main lipids that interact closely with cofilin-1. Both the charge and geometry of the head-group of the PIP2 lipid play important roles in these interactions.
A Theoretical Perspective to Decipher the Origin of High Hydrogen Storage Capacity in Mn(II) Metal-Organic Framework
- First Published: 04 November 2022

Origin of the large hydrogen uptake capacity of Mn(II)-based [(Mn4Cl)3(BTT)8]3−(BTT3−=1,3,5-benzenetristetrazolate) metal-organic framework is studied using periodic density functional theory calculations. The calculations show that there are many strong binding pockets available for hydrogen to bind, thus enhancing the uptake capacity.
Quantum Phase Diagram of a Frustrated Spin-1/2 Ferro-Antiferromagnetic Normal Ladder
- First Published: 31 October 2022

The two-leg ladder model with ferro- and antiferromagnetic exchange interactions along the legs and coupling with ferro- or antiferromagnetic rung interactions is considered here. A DMRG analysis of this model reveals an intriguing phase diagram with five distinct phases. The NCF phase is the most dominant phase, followed by FM, AFM, dimer and m-1/4 phase.
Designing a Propellane-based Nonlinear Optically Active System Absorbing in Three Different Wavelength Regions
- First Published: 24 August 2022

Propellane consists of three wings separated by a saturated common C−C linkage. This makes it an ideal system to design a molecule that can absorb in three different wavelength regions, each corresp-onding to one of the wings. Additionally, if the wings are chosen to be nonlinear optically active then it can pave a path to design an interesting nonlinear optically active material.
Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization
- First Published: 25 October 2022

The electrocyclization of gauche-1,3-Butadiene (GBUT) to Bicyclobutane (BIBUT) and its substituted −F and −CH3 derivatives were studied. The GBUT/F-GBUT to BIBUT/F-BIBUT photoconversion can occur via a conical intersection (CI) geometry, whereas the CH3-GBUT to CH3-BIBUT conversion proceeds via a thermal pathway with a characterized transition state (TS). For all the three systems “on the fly” surface hopping molecular dynamics were performed.
Elucidating the Implications of Diverse Dynamical Responses in p53 Protein
- First Published: 08 October 2022
Oxygen Healing and CO2/H2/Anisole Dissociation on Reduced Molybdenum Oxide Surfaces Studied by Density Functional Theory
- First Published: 18 August 2022
Semiclassical Trajectory Studies of Reactive and Nonreactive Scattering of OH(A 2Σ+) by H2 Based on an Improved Full-Dimensional Ab Initio Diabatic Potential Energy Matrix
- First Published: 18 February 2022

Semiclassical trajectory calculations for the nonadiabatic quenching of OH(A) by H2 on a modified ab initio diabatic potential energy matrix report branching fraction of the adiabatic and nonadiabatic channels and the product internal state distribution in the nonadiabatic quenching channel. The results are in reasonable agreement with experimental and previous quantum calculations.
Multiple Ensembles of the Hydrogen-bonded Network in Ethylammonium Nitrate versus Water from Vibrational Spectral Dynamics of SCN− Probe
- First Published: 14 August 2022

A molecular-level interpretation of the solvation environment associated dynamics and spectroscopic properties of the nitrile stretching mode of the thiocyanate probe in protic ionic liquid, ethylammonium nitrate (EAN) versus water (H2O) from a fast and accurate computational method is reported. The frequency dependence of the reorientation anisotropy dynamics of SCN− within the ionic liquid framework indicates multiple hydrogen-bonding subensembles in EAN as compared to H2O.
Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation
- First Published: 14 October 2022

Binding modes of Glycosaminoglycans (GAGs) with chemokine IL8 were identified. IL8-GAGs bind through favorable electrostatic and non-polar solvation interactions. Multiple minima separated by energy barriers are mainly observed for the bond formation of almost all the GAGs compared to the free states. Both direct and water-mediated IL8-GAG hydrogen-bonded networks suggest that apart from the cationic surface, the interactions could happen through other nonspecific surfaces of IL8.
Construction of Beyond Born-Oppenheimer Based Diabatic Surfaces and Generation of Photoabsorption Spectra: The Touchstone Pyrazine (C4N2H4)
- First Published: 01 September 2022

Beyond Born-Oppenheimer approach is employed to construct diabatic potential energy surfaces of four excited electronic states of pyrazine. Time-Dependent Discrete Variable Representation dynamics is subsequently performed over those surfaces to compute its photoabsorption spectra. Those spectral envelops show better agreement with the experimental ones compared to other theoretical results.
A Tug of War between the Self- and Cross-associating Hydrogen Bonds in Neutral Ammonia-Water Clusters: Energetic Insights by Molecular Tailoring Approach
- First Published: 20 September 2022
Binary Mixtures in Linear Convection Arrays
- First Published: 20 September 2022

Binary mixtures of active-passive particles in convection arrays exhibit a conspicuous phase separation into two distinct colloidal fluids for strong self-propulsion of the active fraction. The passive fluid circulating inside the convection rolls and the active one accumulating in stagnation areas along the array walls. On the other hand, a little fraction of weak active particles exert a strong stirring action on a passive colloidal fluid.
Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations
- First Published: 19 August 2022
Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics
- First Published: 02 September 2022

All-atom molecular dynamics simulations are carried out on amyloid-β (13-42) peptides implementing Hamiltonian replica exchange method with solute tempering. The results reveal conformations that remain inaccessible using experimental techniques. Investigations revealed key interactions that could trigger seed formation required for disease relevant species generation.
Coherence and Efficient Energy Transfer in Molecular Wires: Insights from Surface Hopping Simulations
- First Published: 09 August 2022
Self-Assembling Behaviour of Perylene, Perylene Diimide, and Thionated Perylene Diimide Deciphered through Non-Covalent Interactions
- First Published: 26 July 2022

Successive addition of monomers leads to a consequent rise in the association energy, although to a much greater extent in PDI and t-PDI than in perylene, while the steric interactions in t-PDI quench the cooperativity in its SMP formation. A detailed analysis reveals the presence of π-π, π-hole⋅⋅⋅O=C, and π-hole⋅⋅⋅S=C electrostatic interactions playing crucial role in the self-assembly process.
Effect of Protonation and Deprotonation on Electron Transfer Mediated Decay and Interatomic Coulombic Decay
- First Published: 10 September 2022
Structure and Orientation of Water and Choline Chloride Molecules around a Methane Hydrophobe: A Computer Simulation Study
- First Published: 18 July 2022

Denaturation inhibiting agent choline chloride forces solvent (water) towards methane, which gets reflected in the spatial distribution of water. This arrangement of solvent and the co-solvent results in two populated orientations - tangential and bulk, and affects the tetrahedral hydrogen bonding network of water.
Deciphering the Role of Substitution in Transition-Metal Phosphorous Trisulfide (100) Surface: A Highly Efficient and Durable Pt-free ORR Electrocatalyst
- First Published: 25 April 2022
Influence of Ion Specificity and Concentration on the Conformational Transition of Intrinsically Disordered Sheep Prion Peptide
- First Published: 27 May 2022

Atomistic molecular dynamics simulations are used to investigate the effect of alkali and alkaline metal ions on the trans conformation of the intrinsically disordered region of the cellular prion protein. The Li+ ions at lower concentration is found to efficiently shift the dynamic equilibrium of the disordered protein segment from toxic beta-hairpin state to natural alpha-helical conformation. This ion specific effect is further compromised at higher salt concentration and lower charge density.
2D Homogeneous Holey Carbon Nitride: An Efficient Anode Material for Li-ion Batteries With Ultrahigh Capacity
- First Published: 25 April 2022
Energetic Ordering of Hydrogen Bond Strengths in Methanol-Water Clusters: Insights via Molecular Tailoring Approach
- First Published: 18 March 2022
An Overview of Structure and Dynamics Associated with Hydrophobic Deep Eutectic Solvents and Their Applications in Extraction Processes
- First Published: 14 June 2022

A collective outlook on the most recent advancement in understanding the microstructure and dynamics associated with hydrophobic deep eutectic solvents (HDESs) is presented. An overview on how the integration of experiments and computational techniques can help understand the mechanism of extraction using HDESs is also provided.
Origin of Resonant Character in the Electron Impact Two-Body Neutral-Fragmentation of Methane
- First Published: 04 May 2022

The origin of resonant character in the low energy electron impact two-body neutral fragmentation of methane yielding CH3 radical and a hydrogen atom is reported. This molecular fragmentation by the resonant capture, yielding only neutral fragments, are a manifestation of the autodetachment phenomena during the course of fragmentation reaction.
Strongly Bound π-Hole Tetrel Bonded Complexes between H2SiO and Substituted Pyridines. Influence of Substituents
- First Published: 31 March 2022

Nature of Tetrel Bond: Quantum mechanical is carried out to investigate the strength and nature of the N…Si tetrel bond between H2SiO and substituted pyridines. The strength and nature of the π-hole based N…Si bond is compared with the N…C tetrel bond and N…S chalcogen bond. The effect of substituent on the binding energy is explored. Hyperconjugation interaction between the two units plays significant role in stabilizing the complex. The N…Si tetrel bond is similar to the coordinate covalent bond.
The ‘Quantal Newtonian’ First Law: A Complementary Perspective to the Stationary-state Quantum Theory of Electrons
- First Published: 10 May 2022

A complementary perspective to stationary-state Schrödinger-Pauli/Schrödinger theory of electrons in an electromagnetic field is described. The perspective is that of the individual electron via its equation of motion or ‘Quantal Newtonian’ First Law. The perspective is elucidated by application to semiconductor quantum dots in a magnetic field in a ground, and first excited singlet and triplet states. The relationship of the new perspective to Quantal and traditional density functional theories is briefly explained.
Constructing Potential Energy Surface with Correlated Theory for Dipeptides Using Molecular Tailoring Approach
- First Published: 03 February 2023

Employing a fragment-based molecular tailoring approach, the construction of PES of dipeptides using correlated methods with the computational economy is demonstrated. The MP2/aug-cc-pVTZ and CCSD/aug-cc-pVDZ level PES are constructed for prototype dipeptides viz. alanine-alanine and alanine-proline.
A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II
- First Published: 25 January 2023

The underlying dynamics of binding and unbinding of a ligand to an enzyme and its interactions with amino acid residues modify the enthalpy, entropy, and total binding free energy estimated using a single molecular dynamics trajectory in combination with the molecular mechanics with generalised Born and surface area solvation (MM/GBSA) method.
Glycolytic Wave Patterns in a Simple Reaction-diffusion System with Inhomogeneous Influx: Dynamic Transitions
- First Published: 07 December 2022
Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA
- First Published: 05 January 2023

Multiple Transcription Factors (TFs) search on Nucleosome: The target search efficiency for a pair of TFs on nucleosome DNA relies on nucleosome dynamics, protein-protein complex formation rates, their dissociation kinetics and spatial position of their cognate motifs. Using a discrete-state stochastic theoretical model and Monte Carlo simulation, we elucidate the molecular details of their target search processes.
Insights into the CO2 Capture Capacity of Covalent Organic Frameworks
- First Published: 23 January 2023

An inexpensive computational method is developed to unravel the structure-property relationship of complex covalent organic framework (COFs) molecules toward CO2 capture. The model is tested on boronic acid derived COFs. Increasing the number of −NH2 attached to aromatic moiety makes COFs better candidates for CO2 capture at room temperature and an increase in the size of the aromatic ring facilitates CO2 capture at high pressure.
Vibrational Sum Frequency Generation Spectra of Water-Vapor Interfaces Covered by Alcohols: Effects of Surface Coverage and Coupling between Oscillators
- First Published: 20 December 2022

Vibrational sum frequency generation spectra of water are calculated for air-water interfaces covered by alcohol molecules for different surface coverages. Two different alcohols of varying hydrophobic parts are considered and the spectral features are connected to the interfacial structure and interactions. The effects of coupling between vibrational modes of interest are also presented.
Tunnelling Dynamics of Kicked Systems: A Route to Tunnelling Control
- First Published: 10 January 2023

Complete destruction of tunnelling (CDT) can only be achieved with continuous temporal perturbation on symmetric double and triple well model quantum systems. The discontinuous one shows tunnelling without CDT or over-barrier transition, depending on the nature of reversal time, whether fixed or random, and the spatial symmetry of applied perturbation.