المؤلفون: Domínguez-Flores, Fabiola, Kiljunen, Toni, Groß, Axel, Sakong, Sung, Melander, Marko M.

مصطلحات موضوعية: density functional theory, molecular dynamics, quantum mechanical/molecular mechanical calculations, thermodynamics, computational methods, liquid solid interfaces, catalysts and catalysis, solvation, termodynamiikka, tiheysfunktionaaliteoria, rajapinnat (pinnat), rajapintailmiöt, simulointi, molekyylidynamiikka, pintakemia

وصف الملف: application/pdf; fulltext

Relation: Journal of Chemical Physics; 161; 338228; 307853; Research Council of Finland; Suomen Akatemia; CONVID_233315622

الاتاحة: http://urn.fi/URN:NBN:fi:jyu-202409115912

المؤلفون: Timothy J. Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M. York

مصطلحات موضوعية: Molecular Biology, Physiology, Statistics, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, whereas approaches like, umbrella potential placement, free energy profile, efficiently optimize low, dimensional reaction pathways, >- transphosphorylation reaction, expensive quantum mechanical, previous string iterations, modified string method, accelerated string method, free energy surface, current best estimate, aggregate sampling obtained, synthetic images used, string method, sampling obtained, tautomeric reaction, molecular mechanical, images used, sampling performed, perform sampling, available sampling, three algorithms

Relation: https://figshare.com/articles/journal_contribution/Surface-Accelerated_String_Method_for_Locating_Minimum_Free_Energy_Paths/25238357

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01401.s001
https://figshare.com/articles/journal_contribution/Surface-Accelerated_String_Method_for_Locating_Minimum_Free_Energy_Paths/25238357

المؤلفون: Zacharias Liasi, Lasse Jensen, Kurt V. Mikkelsen

مصطلحات موضوعية: Biophysics, Medicine, Cell Biology, Genetics, Molecular Biology, Biotechnology, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, templated silver nanocluster, stabilized silver nanoclusters, molecular mechanics approach, molecular mechanical approach, including ligand fragmentation, hybrid quantum mechanical, combined quantum mechanics, atomic properties used, properties used, unique optical, optical properties, novel systems, nanomaterial due, important parameter, experimental data, electronic properties, efficient methods

Relation: https://figshare.com/articles/journal_contribution/A_Combined_Quantum_Mechanics_and_Molecular_Mechanics_Approach_for_Simulating_the_Optical_Properties_of_DNA-Stabilized_Silver_Nanoclusters/24925272

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01022.s001
https://figshare.com/articles/journal_contribution/A_Combined_Quantum_Mechanics_and_Molecular_Mechanics_Approach_for_Simulating_the_Optical_Properties_of_DNA-Stabilized_Silver_Nanoclusters/24925272

المؤلفون: Jiayun Zhong, Alexander V. Soudackov, Sharon Hammes-Schiffer

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Molecular Biology, Sociology, Infectious Diseases, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, insights provide guidance, free energy simulations, coupled electron transfer, hybrid quantum mechanical, fourth pcet reaction, enzyme ribonucleotide reductase, four pcet reactions, ribonucleotide reductase, molecular mechanical, whereas pcet, pcet reactions, interfacial pcet, slightly exoergic, probing nonadiabaticity, intermediate regime, guanosine diphosphate, fully adiabatic, electronically nonadiabatic, dna synthesis

Relation: https://figshare.com/articles/journal_contribution/Probing_Nonadiabaticity_of_Proton-Coupled_Electron_Transfer_in_Ribonucleotide_Reductase/25148238

الاتاحة: https://doi.org/10.1021/acs.jpclett.3c03552.s001
https://figshare.com/articles/journal_contribution/Probing_Nonadiabaticity_of_Proton-Coupled_Electron_Transfer_in_Ribonucleotide_Reductase/25148238

المؤلفون: Bourne-Worster, Susannah, Worth, Graham A

المصدر: The Journal of Chemical Physics , 160 (6) , Article 065102. (2024)

مصطلحات موضوعية: Excited states, Potential energy surfaces, Quantum mechanical/molecular mechanical calculations, Computational methods, Kinetic isotope effects, Photoexcitations, Excited state reaction dynamics, Quantum tunneling, Biophysical chemistry, Proteins

وصف الملف: application/pdf

Relation: https://discovery.ucl.ac.uk/id/eprint/10187458/1/065102_1_5.0188834.pdf; https://discovery.ucl.ac.uk/id/eprint/10187458/

الاتاحة: https://discovery.ucl.ac.uk/id/eprint/10187458/1/065102_1_5.0188834.pdf
https://discovery.ucl.ac.uk/id/eprint/10187458/

المؤلفون: Grisafi, Andrea, Salanne, Mathieu

المساهمون: Institut des Sciences du Calcul et des Données (ISCD), Sorbonne Université (SU), Institut universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), PHysicochimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ANR-22-PEBA-0002,BATMAN,BATteries: data Mining, Artificial intelligence and digital twins for the Next generation(2022)

المصدر: ISSN: 0021-9606.

مصطلحات موضوعية: Density functional theory, Molecular dynamics, Quantum mechanical/molecular mechanical calculations, Ewald summation, Electrostatics, Machine learning, Electrochemistry, Electrolytes, Electrical double layers, Catalysts and Catalysis, [CHIM]Chemical Sciences, [PHYS]Physics [physics]

Relation: info:eu-repo/semantics/altIdentifier/arxiv/2405.07370; hal-04643797; https://hal.sorbonne-universite.fr/hal-04643797; https://hal.sorbonne-universite.fr/hal-04643797/document; https://hal.sorbonne-universite.fr/hal-04643797/file/JCP24-AR-02019.pdf; ARXIV: 2405.07370

الاتاحة: https://hal.sorbonne-universite.fr/hal-04643797
https://hal.sorbonne-universite.fr/hal-04643797/document
https://hal.sorbonne-universite.fr/hal-04643797/file/JCP24-AR-02019.pdf
https://doi.org/10.1063/5.0218379

المؤلفون: Judit Katalin Szántó, Johannes C. B. Dietschreit, Mikhail Shein, Anne K. Schütz, Christian Ochsenfeld

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Inorganic Chemistry, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, sufficiently large averages, provide crucial support, nuclear magnetic resonance, multiple nucleotide states, important atomistic insights, representative structural ensembles, study sheds light, experimental nmr signals, 31 , protein environment nmr, mm structure optimizations, mm molecular dynamics, structural environment, protein environment, nmr measurements, molecular mechanical, experimental spectra, mm study, spectroscopy allows, reliable assignments, quantum mechanical, probe experimentally

Relation: https://figshare.com/articles/journal_contribution/Systematic_QM_MM_Study_for_Predicting_sup_31_sup_P_NMR_Chemical_Shifts_of_Adenosine_Nucleotides_in_Solution_and_Stages_of_ATP_Hydrolysis_in_a_Protein_Environment/25428661

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01280.s001

المؤلفون: Ming-Yu Yang, Xin-Ping Wu

مصطلحات موضوعية: Biophysics, Biochemistry, Space Science, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, relatively high accuracy, popular tool due, low computational cost, ionically bonded systems, quantum mechanical region, 9 , 14 , future chemical studies, e ., mg, combined quantum mechanical, excellent performance holds, metal oxides using, shifted embedded cluster, embedded cluster method, metal oxides, embedded cluster, molecular mechanical, overall performance, various adsorbates, validation calculations, thereby enabling

Relation: https://figshare.com/articles/journal_contribution/Level-Shifted_Embedded_Cluster_Method_for_Modeling_the_Chemistry_of_Metal_Oxides/25127573

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01123.s001

المؤلفون: van Keulen, S. C., Martin, J., Colizzi, F., Frezza, E., Trpevski, Daniel, Diaz, N. C., Vidossich, P., Rothlisberger, U., Hellgren Kotaleski, J., Wade, R. C., Carloni, P.

المصدر: WIREs Computational Molecular Science. 13(1)

مصطلحات موضوعية: Binding energy, Bioinformatics, Computational chemistry, Enzymes, Free energy, Molecular modeling, Molecular structure, Monte Carlo methods, Quantum theory, Rate constants, Statistical mechanics, Adenylyl cyclase, Catalyse, Free energy simulations, Isoforms, Molecular simulations, Quantum mechanical/molecular mechanical, Signaling cascades, Sub-cellular, System biology modeling, Systems biology, Molecular dynamics, adenylyl cyclases, molecular simulation, systems biology modeling

وصف الملف: print

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-324730
https://doi.org/10.1002/wcms.1623

المؤلفون: Yao Cai, Xia Mu, Guohui Li, Dingguo Xu

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Physiology, Biotechnology, Hematology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, zinc bifunctional enzyme, mechanistic insights garnered, limiting step within, isomeric conjugate (<, general base catalyst, general acid catalyst, epoxy ring opening, epoxy oxygen atom, computations firmly support, na stages constitute, molecular mechanical elucidation, leukotriene a4 hydrolase, active site ’, entire epoxidase mechanism, lta4h catalytic role, catalytic mechanism, quantum mechanical, na ), lta4h ’

Relation: https://figshare.com/articles/journal_contribution/Quantum_Mechanical_Molecular_Mechanical_Elucidation_of_the_Catalytic_Mechanism_of_Leukotriene_A4_Hydrolase_as_an_Epoxidase/24639462

الاتاحة: https://doi.org/10.1021/acs.jpcb.3c05969.s001
https://figshare.com/articles/journal_contribution/Quantum_Mechanical_Molecular_Mechanical_Elucidation_of_the_Catalytic_Mechanism_of_Leukotriene_A4_Hydrolase_as_an_Epoxidase/24639462

المؤلفون: Farzad Molani, Simon Webb, Art E. Cho

مصطلحات موضوعية: Biophysics, Biochemistry, Physiology, Pharmacology, Biotechnology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, specified atomic charges, proposed pose using, overall pearson correlation, mining minima approach, mechanically recalculated ones, drug discovery campaigns, classical mining minima, 147 different ligands, mean unsigned error, incorporates quantum mechanical, square error, molecular mechanical, methods examined, limited set, implicit solvent, force fields, fep +, explicit water, combined accuracy, based methods, 75 kcal, 39 kcal

Relation: https://figshare.com/articles/journal_contribution/Combining_QM_MM_Calculations_with_Classical_Mining_Minima_to_Predict_Protein_Ligand_Binding_Free_Energy/22669787

الاتاحة: https://doi.org/10.1021/acs.jcim.2c01637.s001
https://figshare.com/articles/journal_contribution/Combining_QM_MM_Calculations_with_Classical_Mining_Minima_to_Predict_Protein_Ligand_Binding_Free_Energy/22669787

المؤلفون: Masaki Tsujimura (9147607), Minaka Sugano (14341358), Hiroshi Ishikita (199546), Keisuke Saito (516747)

مصطلحات موضوعية: Biophysics, Cell Biology, Molecular Biology, Physiology, Ecology, Cancer, Inorganic Chemistry, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, dissipation modes depending, >- binding protein, molecular mechanical approach, light conditions leads, harvesting antenna proteins, calculated absorption wavelength, absorption wavelength, quantum mechanical, use light, soret band, results suggest, red shift, porphyrin ring, lumenal side, light intensity, green region, changes upon, changes owing, candidate component, acrylate group

Relation: https://figshare.com/articles/journal_contribution/Mechanism_of_Absorption_Wavelength_Shift_Depending_on_the_Protonation_State_of_the_Acrylate_Group_in_Chlorophyll_i_c_i_/21831869

الاتاحة: https://doi.org/10.1021/acs.jpcb.2c07232.s001

المؤلفون: Soataliyev Diyorbek Bahodir ogli

المصدر: Academic Research Journal, 1(1), 156-159, (2022-06-04)

مصطلحات موضوعية: Operation without damage, repair, technical condition, wear, wear and tear, corrosion, wear resistance, friction, deformation, mechanical wear, molecular-mechanical wear, corrosion-mechanical wear, fretting-corrosion, cavitation wear, erosion erosion, erosion results, erosion intensity

Relation: https://doi.org/10.5281/zenodo.6612768; https://doi.org/10.5281/zenodo.6612769; oai:zenodo.org:6612769

الاتاحة: https://doi.org/10.5281/zenodo.6612769

المؤلفون: Tao E. Li (5810465), Sharon Hammes-Schiffer (1274832)

مصطلحات موضوعية: Biophysics, Evolutionary Biology, Inorganic Chemistry, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, selective infrared photochemistry, modify chemical reactions, energy transfer pathways, energy transfer pathway, co )< sub, berry pseudorotation reaction, axial co vibrations, achieve linear scaling, hybrid quantum mechanical, 5 , qm solute molecule, cavity molecular dynamics, molecular mechanical, n <, cavity effect, wide range, strongly exciting, simulations predict, selectively excites, recent two, polaritonic systems, novel means

Relation: https://figshare.com/articles/journal_contribution/QM_MM_Modeling_of_Vibrational_Polariton_Induced_Energy_Transfer_and_Chemical_Dynamics/21785347

الاتاحة: https://doi.org/10.1021/jacs.2c10170.s001

المؤلفون: Xingfan Zhang (6276953), Lei Zhu (16642), Qing Hou (8995262), Jingcheng Guan (7123832), You Lu (154239), Thomas W. Keal (1298871), John Buckeridge (1298874), C. Richard A. Catlow (7163117), Alexey A. Sokol (1298880)

مصطلحات موضوعية: Biophysics, Cell Biology, Genetics, Molecular Biology, Developmental Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, predicted formation energies, oxygen vacancies accompanied, findings provide opportunities, certain charged states, hybrid quantum mechanical, relevant charged defects, density functional theory, 2 , pure mm level, charged defects, molecular mechanical, mm level, widely used, wide range, theory reach, structure calculations, solids using, scale modeling, polarizable shell, physical properties

Relation: https://figshare.com/articles/journal_contribution/Toward_a_Consistent_Prediction_of_Defect_Chemistry_in_CeO_sub_2_sub_/21766569

الاتاحة: https://doi.org/10.1021/acs.chemmater.2c03019.s001

المؤلفون: Xitong Song (5073782), Jia Liu (41593), Binju Wang (1419697)

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Biotechnology, Science Policy, Computational Biology, Environmental Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, regulated electron transfer, nonheme diiron oxygenases, geminal diolate intermediate, bridging oh ligand, – p formation, using quantum mechanics, phnz would expand, organophosphonate catabolism mechanisms, initial oxygen activation, fe1 ­( iv, molecular mechanical study, quantum mechanical, oxygen activation, molecular mechanics, study demonstrates, phnz organophosphonate, catabolism constitutes, >)- oh, yet understood, r <

Relation: https://figshare.com/articles/journal_contribution/Emergence_of_Function_from_Nonheme_Diiron_Oxygenases_A_Quantum_Mechanical_Molecular_Mechanical_Study_of_Oxygen_Activation_and_Organophosphonate_Catabolism_Mechanisms_by_PhnZ/18858648

الاتاحة: https://doi.org/10.1021/acscatal.1c05116.s001

المؤلفون: Shiqing Zhang (652535), Xinyi Li (1778476), Yijing Wang (227101), Jingjing Wei (478970), Xue Zhang (166886), Yongjun Liu (291644)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Cancer, Infectious Diseases, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, resolution crystal structure, prior electron transfer, biochemical evidence showed, mutant study indicates, molecular mechanical calculations, peroxygenase mechanism catalyzed, hydrogen atom abstraction, hemoglobin dehaloperoxidase involved, peroxygenase mechanism, hemoglobin dehaloperoxidase, quantum mechanical, computational study, triggered either, titratable residues, quartet state, previously suggested, porphyrin group, multifunctional hemoprotein, limiting step, hydroxyl group, feasibility depends

Relation: https://figshare.com/articles/journal_contribution/Computational_Study_of_the_Peroxygenase_Mechanism_Catalyzed_by_Hemoglobin_Dehaloperoxidase_Involved_in_the_Degradation_of_Chlorophenols/19071256

الاتاحة: https://doi.org/10.1021/acs.inorgchem.1c03721.s001

المؤلفون: Moubarak, Samah, Rippers, Yvonne, Elghobashi-Meinhardt, Nadia, Mroginski, Maria Andrea

مصطلحات موضوعية: density functional theory calculations, structural biology, computational modeling, metalloenzyme active site, electronic properties, sulerythrin, quantum mechanical/molecular mechanical (QM/MM) computations, ddc:570

وصف الملف: 18 Seiten; application/pdf

Relation: https://refubium.fu-berlin.de/handle/fub188/36940; http://dx.doi.org/10.17169/refubium-36653

الاتاحة: https://refubium.fu-berlin.de/handle/fub188/36940
https://doi.org/10.17169/refubium-36653
https://doi.org/10.3389/fmolb.2022.945415

المؤلفون: Sayibjan Sadikovich Negmatov, Nodira Sayibjanovna Abed, Giyas Gulyamovich Gulyamov, Olim Kholikulovich Eshkobilov

المصدر: RA JOURNAL OF APPLIED RESEARCH, 07(11), 2672-2679, (2021-11-22)

مصطلحات موضوعية: Molecular-mechanical theory of friction, molecular-mechanoelectric theory of friction, molecular component, electrical component, contact

Relation: https://doi.org/10.47191/rajar/v7i11.09; oai:zenodo.org:5717570

الاتاحة: https://doi.org/10.47191/rajar/v7i11.09

المؤلفون: Manoj Mandal (8156265), Keisuke Saito (516747), Hiroshi Ishikita (199546)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Cell Biology, Genetics, Molecular Biology, Physiology, Evolutionary Biology, Immunology, Inorganic Chemistry, Virology, Computational Biology, Chemical Sciences not elsewhere classified, subsequent proton transfer, report proton transfer, redox potential (<, making electron transfer, molecular mechanical approach, 2 +, ), (, 5 , 4 , 3 , 2 , tyrz energetically uphill, sup >–, substrate water molecule, psii ), cl

Relation: https://figshare.com/articles/journal_contribution/Requirement_of_Chloride_for_the_Downhill_Electron_Transfer_Pathway_from_the_Water-Splitting_Center_in_Natural_Photosynthesis/17679392

الاتاحة: https://doi.org/10.1021/acs.jpcb.1c09176.s001