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This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.

Chemistry, Physical and theoretical. --- Physical chemistry. --- Bioinformatics . --- Computational biology . --- Spectroscopy. --- Proteins . --- Theoretical and Computational Chemistry. --- Physical Chemistry. --- Computer Appl. in Life Sciences. --- Spectroscopy/Spectrometry. --- Protein Science. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Chemistry, Theoretical --- Physical chemistry --- Theoretical chemistry --- Chemistry --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Analysis, Spectrum --- Spectra --- Spectrochemical analysis --- Spectrochemistry --- Spectrometry --- Spectroscopy --- Chemistry, Analytic --- Interferometry --- Optics --- Radiation --- Wave-motion, Theory of --- Absorption spectra --- Light --- Spectroscope --- Bioinformatics --- Data processing --- Qualitative --- Analytical chemistry --- Photobiology. --- Photochemistry

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This book describes the results of both theoretical and experimental research on many topical issues in intramolecular hydrogen bonding. Its great advantage is that the presented research results have been obtained using many different techniques. Therefore, it is an excellent review of these methods, while showing their applicability to the current scientific issues regarding intramolecular hydrogen bonds. The experimental techniques used include X-ray diffraction, infrared and Raman spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), nuclear quadrupole resonance spectroscopy (NQR), incoherent inelastic neutron scattering (IINS), and differential scanning calorimetry (DSC). The solvatochromic and luminescent studies are also described. On the other hand, theoretical research is based on ab initio calculations and the Car–Parrinello Molecular Dynamics (CPMD). In the latter case, a description of nuclear quantum effects (NQE) is also possible. This book also demonstrates the use of theoretical methods such as Quantum Theory of Atoms in Molecules (QTAIM), Interacting Quantum Atoms (IQA), Natural Bond Orbital (NBO), Non-Covalent Interactions (NCI) index, Molecular Tailoring Approach (MTA), and many others.

Research & information: general --- intramolecular interaction --- interaction energy --- hydrogen bond --- intramolecular hydrogen bonds --- deuterium isotope effects on chemical shifts --- isotope ratios --- hydrogen bond energies --- intramolecular hydrogen bonding --- high-accuracy extrapolation methods --- QTAIM --- non-covalent interactions --- local vibrational modes --- hydrogen bond (HB) --- intramolecular hydrogen bond (IHB) --- molecular tailoring approach (MTA) --- fragmentation methods --- bond energy estimation --- noncovalent interactions --- structures and binding energies --- charge-transfer interactions --- spin–spin coupling constants --- polymorphism --- isomerization --- phase transition --- nitro group --- matrix isolation --- IINS --- FT-IR --- Raman --- X-ray --- NQR --- DSC --- DFT --- Schiff base --- N-salicylidene aniline derivative --- photophysical properties --- solvatochromism --- Hirshfeld surface analysis --- amino-alcohols --- α-substitution --- beryllium bonds --- calculated infrared spectra --- interacting quantum atoms --- resonance-assisted hydrogen bond --- Schiff bases --- inelastic incoherent neutron scattering --- isotopic effect --- excited-state intramolecular proton transfer --- photochemistry --- photobiology --- quantum chemistry --- molecular dynamics --- ultrafast processes --- gas phase --- crystalline phase --- MP2 --- CCSD --- AIM --- SAPT --- nuclear quantum effects --- CPMD --- n/a --- spin-spin coupling constants

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This book describes the results of both theoretical and experimental research on many topical issues in intramolecular hydrogen bonding. Its great advantage is that the presented research results have been obtained using many different techniques. Therefore, it is an excellent review of these methods, while showing their applicability to the current scientific issues regarding intramolecular hydrogen bonds. The experimental techniques used include X-ray diffraction, infrared and Raman spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), nuclear quadrupole resonance spectroscopy (NQR), incoherent inelastic neutron scattering (IINS), and differential scanning calorimetry (DSC). The solvatochromic and luminescent studies are also described. On the other hand, theoretical research is based on ab initio calculations and the Car–Parrinello Molecular Dynamics (CPMD). In the latter case, a description of nuclear quantum effects (NQE) is also possible. This book also demonstrates the use of theoretical methods such as Quantum Theory of Atoms in Molecules (QTAIM), Interacting Quantum Atoms (IQA), Natural Bond Orbital (NBO), Non-Covalent Interactions (NCI) index, Molecular Tailoring Approach (MTA), and many others.

intramolecular interaction --- interaction energy --- hydrogen bond --- intramolecular hydrogen bonds --- deuterium isotope effects on chemical shifts --- isotope ratios --- hydrogen bond energies --- intramolecular hydrogen bonding --- high-accuracy extrapolation methods --- QTAIM --- non-covalent interactions --- local vibrational modes --- hydrogen bond (HB) --- intramolecular hydrogen bond (IHB) --- molecular tailoring approach (MTA) --- fragmentation methods --- bond energy estimation --- noncovalent interactions --- structures and binding energies --- charge-transfer interactions --- spin–spin coupling constants --- polymorphism --- isomerization --- phase transition --- nitro group --- matrix isolation --- IINS --- FT-IR --- Raman --- X-ray --- NQR --- DSC --- DFT --- Schiff base --- N-salicylidene aniline derivative --- photophysical properties --- solvatochromism --- Hirshfeld surface analysis --- amino-alcohols --- α-substitution --- beryllium bonds --- calculated infrared spectra --- interacting quantum atoms --- resonance-assisted hydrogen bond --- Schiff bases --- inelastic incoherent neutron scattering --- isotopic effect --- excited-state intramolecular proton transfer --- photochemistry --- photobiology --- quantum chemistry --- molecular dynamics --- ultrafast processes --- gas phase --- crystalline phase --- MP2 --- CCSD --- AIM --- SAPT --- nuclear quantum effects --- CPMD --- n/a --- spin-spin coupling constants

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Molecular simulations are commonly used in physics, chemistry, biology, material science, engineering, and even medicine. This book provides a wide range of molecular simulation methods and their applications in various fields. It reflects the power of molecular simulation as an effective research tool. We hope that the presented results can provide an impetus for further fruitful studies.

Technology: general issues --- molecular dynamics simulation --- osmosis --- water transport --- nanochannel --- carbon nanotube --- graphene --- osmolyte --- compartment --- rhodopsins --- spectral properties of rhodopsins --- spectral tuning in rhodopsins --- engineering of red-shifted rhodopsins --- photobiology --- biological photosensors --- molecular modeling --- multiscale --- coarse graining --- Monte Carlo simulation --- force fields --- neural network --- many body interactions --- sampling --- local sampling --- local free energy landscape --- generalized solvation free energy --- molecular solvation theory --- three-dimensional reference interaction site model --- Kovalenko-Hirata closure --- biomolecular simulation --- multiple time step MD --- protein-ligand binding --- biomolecular solvation --- antibody --- epitope --- molecular dynamics --- mutation --- toll-like receptor --- GPU programming --- DNA damage --- proton transport --- drag reduction --- surfactant molecules --- self-assembly --- coarse-grained molecular simulation --- numerical method --- laser-matter interaction --- time-dependent Schrödinger equation --- time-dependent unitary transformation method --- strong-field ionization --- Kramers-Henneberger frame --- hairy nanoparticles --- adsorption on nanoparticles --- nanocarriers --- computer simulations --- COVID-19 --- SARS-CoV-2 --- PF-07321332 --- α-ketoamide --- 3CL protease --- main protease --- DFT --- CASTEP --- aiMD --- ab initio molecular dynamics --- phase transition --- polymorphism --- Janus particles --- phase transitions --- gemini --- force field --- parametrisation --- antimicrobial --- membranes --- colloids with competing interactions --- periodic microphases --- confinement --- Monte Carlo --- atomistic simulation --- molecular simulation --- hard sphere --- extreme conditions --- nanocomposites --- cluster --- crystallization --- atomic structure --- packing --- semi-flexible polymers --- order parameter --- n/a --- time-dependent Schrödinger equation --- Technology.