2023 HBond Bologna - ProkopHapala/FireCore GitHub Wiki

2023 HBond Bologna

By People

• Giovanni Bistoni

  • ORCA develoler - DLPNO-CCSD(T)

• Daniele Fazzi

  • Organic Electronics simualtions of charge-transport
    • Daniele Fazzi, Google Scholar
  • TIDE – Template-Designed Organic Electronics

• TIDE – Template-Designed Organic Electronics

  • Daniele Fazzi
  • Daniele Fazzi, Google Scholar

• Fold-Halo - Halogend bonds in protein folding

• Prof. Dr. Célia Fonseca Guerra - computational rationalization (design principles) of H-Bonds

  • researchgere
  • ORCID
  • Google Scholar
  • The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths
  • Hydrogen-Bond Strength of CC and GG Pairs Determined by Steric Repulsion: Electrostatics and Charge Transfer Overruled
  • Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Rationalization of Hydrogen Bonds

• H-Bond analysis and decomposition schemes (QTAIM,RDG etc.)

  • An Introduction to the Quantum Theory of Atoms in Molecules(QTAIM)
  • PyMol-QTAIM - his works with outputs from the QTAIM program AIMAll.
  • AIMAll - AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.
  • QTAIM presentation by Cina Foroutan-Nejad
  • Intramolecular Hydrogen Bonds: the QTAIM and ELF Characteristics
  • QTAIM Analysis in the Context of Quasirelativistic Quantum Calculations
  • Can QTAIM Topological Parameters Be a Measure of Hydrogen Bonding Strength?
  • Local potential energy: A novel QTAIM tool to quantify the binding energy of classical hydrogen bonds
  • Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations
  • Electron Density Characteristics in Bond Critical Point (QTAIM) versus Interaction Energy Components (SAPT): The Case of Charge-Assisted Hydrogen Bonding
  • RDG - Reduced Density Gradient
  • Investigation of Structures, QTAIM, RDG, ADMET, and docking properties of SASC compound using experimental and theoretical approach

• Cooperativity in H-bonds C. Fonseca

  • The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths
  • Hydrogen-Bond Strength of CC and GG Pairs Determined by Steric Repulsion: Electrostatics and Charge Transfer Overruled
  • Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex
  • Origin of cooperativity in hydrogen bonding

• DNA nucleobase pairs review-Paolo

  • A Density Functional Theory and Information-Theoretic Approach Study of Interaction Energy and Polarizability for Base Pairs and Peptides
  • Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions
  • Cooperative Hydrogen-Bonding in Adenine−Thymine and Guanine−Cytosine Base Pairs. Density Functional Theory and Møller−Plesset Molecular Orbital Study

Global Optimization

• CREST: Conformer–Rotamer Ensemble Sampling Tool

  • Stefan Grimme. We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed.
  • Fast Screening of Minimum Energy Crossing Points with Semiempirical Tight-Binding Methods
  • Automated exploration of the low-energy chemical space with fast quantum chemical methods
  • CREST github

• ASH is a Python-based computational chemistry and multiscale modelling program

• MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations

• Philippe Carbonnière: Structure prediction of nanoclusters from global optimization techniques: Computational strategies and connection to experiments

Computational Methods ( r2SCAN-3c, DLPNO-CCSD(T), ωB97X, F12-basiset )

• r2SCAN-3c: A “Swiss army knife” composite electronic-structure method

• Optimization of the r2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets

• DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes

  • ORCA: DLPNO-CCSD(T) Calculation
  • examle in ORCA DLPNO-CCSD(T)

• ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

• A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions

• MP2-F12 Basis Set Convergence near the Complete Basis Set Limit: Are h Functions Sufficient?