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The PDF copies provided on this page are for preview only. For copyright reasons, you are not allowed to download them. If you wish to get a copy of any of the publications, please contact Elfi Kraka and specify your e-mail address. We will be happy to send you a hard-copy of the publication.
- Crystal Structure of 1-propanethiol–Co2(dobdc) from Laboratory X-ray Powder Diffraction Data,
J. Lefton, K. Pekar, D. Sethio, E. Kraka and T. Runčevski,
Powder Diffraction, 35, 1-6 (2020).
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- Metal–Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy,
V. Oliveira, B. Marcial, F. Machado and E. Kraka,
Materials 13, 55-1-55-23 (2020).
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- SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction,
N. Verma, X. Qu, F. Trozzi, M. Elsaied, N. Karki, Y. Tao, B. Zoltowski, E. C. Larson and E. Kraka,
Int. J. Mol. Sci., 22, 1392-1-1392-27 (2021).
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- Modified Density Functional Dispersion Correction for Inorganic Layered MFX Compounds (M = Ca, Sr, Ba, Pb and X = Cl, Br, I),
D. Sethio, J. Martins, L. M. Lawson Daku, H. Hagemann and E. Kraka,
J. Phys. Chem. A, 124, 1619-1633 (2020).
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- Local vibrational force constants - from the assessment of empirical force constants to the description of bonding in large systems,
W. Zou, Y. Tao, M. Freindorf, D. Cremer and E. Kraka,
Chem. Phys. Lett., 748, 137337-1-137337-9 (2020).
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- Systematic description of molecular deformations with Cremer-Pople puckering and deformation coordinates utilizing analytic derivatives: applied to cycloheptane, cyclooctane, and cyclo[18]carbon,
W. Zou, T. Tao, and E. Kraka,
J. Chem. Phys., 152, 154107-1-154107-15 (2020).
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- Describing Polytopal Rearrangements of Fluxional Molecules with Curvilinear Coordinates Derived from Normal Vibrational Modes: A Conceptual Extension of Cremer−Pople Puckering Coordinates,
W. Zou, T. Tao, and E. Kraka,
J. Chem. Theory Comput., 16, 3162-3192 (2020).
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- In Situ Assessment of Intrinsic Strength of X-I• • • OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory,
Y. Tao, Y. Qiu, W. Zou, S. Nanayakkara, S. Yannacone, and E. Kraka,
Molecules, 25, 1589-1-1589-22 (2020).
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- Quantitative Assessment of Intramolecular Hydrogen Bonds in Neutral Histidine,
S. Yannacone, D. Sethio, and E. Kraka,
Theor. Chem. Acc., 139, 125-1-125-10 (2020).
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- Metal-Ring Interactions in Actinide Sandwich Compounds: A Combined Normalized Elimination of the Small Component and Local Vibrational Mode Study,
M. Makoś, W. Zou, M. Freindorf, and E. Kraka,
Mol. Phys., 118, e1768314 (2020).
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- A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory,
N. Verma, Y. Tao, W. Zou, Xia Chen, Xin Chen, M. Freindorf, and E. Kraka,
Sensors, 20, 2358-1-2358-24 (2020).
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- Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory,
E. Kraka, W. Zou, and Y. Tao,
WIREs: Comput. Mol. Sci., e1480-1-e1480-34 (2020).
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- Characterizing the Metal Ligand Bond Strength via Vibrational Spectroscopy: The Metal Ligand Electronic Parameter (MLEP),
E. Kraka and M. Freindorf,
In Topics in Organometallic Chemistry - New Directions in the Modeling of Organometallic Reactions, A. Lledos and G. Ujaque, Eds.: Springer, New York, 1-43 (2020); DOI: doi.org/10.1007/3418_2020_48.
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- Critical assessment of the FeC and CO bond strength in carboxymyoglobin - A QM/MM Local Vibrational Mode Study,
M. Freindorf and E. Kraka,
J. Mol. Model., 26, 281-1-281-15 (2020).
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- Predicting Potential SARS-COV-2 Drugs - In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking,
N. Komal Karki, N. Verma, F. Trozzi, P. Tao, E. Kraka and B. Zoltowski,
J. Mol. Sci., 22, 1573-1-1573-17 (2021).
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- Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T),
J. Martins, R. P. Quintino, J. R. S. Politi, D. Sethio, R. Gargano, and E. Kraka,
Spectrochim. Acta A, 239, 118540-1-118540-9 (2020).
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- Chelation-Assisted Selective Etching Construction of Hierarchical Polyoxometalate-Based Metal−Organic Frameworks,
Z. Zhang, Y. Tao, H. Tian, Q. Yue, Shumei Liu, Y. Liu, X. Li, Y. Lu, Z. Sun, E. Kraka, and Shuxia Liu,
Chem. Mater. 32, 5550-5557 (2020).
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- Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)- A Review,
E. Kraka, W. Zou, Y. Tao, and M. Freindorf,
Catalysts, 10, 691-1-691-32 (2020).
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- Local Vibrational Mode Analysis of π-Hole Interactions between Aryl Donors and Small Molecule Acceptors,
S. Yannacone, M. Freindorf, Y. Tao, W. Zou, and E. Kraka,
Crystals, 10, 556-1-556-25 (2020).
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- A revised formulation of the generalized subsystem vibrational analysis (GSVA),
Y. Tao, W. Zou, S. Nanayakkara, M. Freindorf, and E. Kraka,
Theor. Chem. Acc., 140, 31-1-31-5 (2021).
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- Comment on: "Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory",
S. Nanayakkara, Y. Tao, and E. Kraka,
J. Comput. Chem. 1-6 (2020).
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- PyVibMS: A PyMOL plugin for visualizing vibrations in molecules and solids,
Y. Tao, W. Zou, S. Nanayakkara, and E. Kraka,
J. Mol. Model. 26, 290-1-290-12 (2020).
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- Equilibrium Geometries, Adiabatic Excitation Energies and Intrinsic C=C/C-H Bond Strengths of Ethylene in Lowest Singlet Excited States Described by TDDFT,
Y. Tao, L. Zhang, W. Zou, and E. Kraka,
Symmetry, 12, 1545–1–1545–13 (2020).
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- Modeling Hydrogen release from water with Borane and Alane catalysts: A Unified Reaction Valley Approach,
S. Nanayakkara, M. Freindorf, Y. Tao, and E. Kraka,
J. Phys. Chem. A, 124, 8978-8993 (2020).
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- Peritectic Phase Transition of Benzene and Acetonitrile into a Cocrystal Relevant to Titan, Saturn's Moon,
C. McConville, Y. Tao, H. Evans, B. Trump, J. B. Lefton, W. Xu, A. Yakovenko, E. Kraka, C. Brown, and T. Runčevski,
Chem. Comm., 56, 13520-13523 (2020).
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- Local Vibrational Mode Analysis of Ion-Solvent and Solvent-Solvent Interactions for Hydrated Ca2+ Clusters,
A. A. A. Delgado, D. Sethio, I. Munar, V. Aviyente, and E. Kraka,
J. Chem. Phys. 153, 224303-1-224303-11 (2020).
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- Deep learning-based ligand design using shared latent implicit fingerprints from collaborative filtering,
R. Srinivas, N. Verma, E. Kraka, and E. C. Larson,
Chem. Inf. Model., 61, 2159-2174 (2021).
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- Mechanosynthesis of a Coamorphous Formulation of Creatine with Citric Acid and Humidity–Mediated Transformation into a Cocrystal,
K. B. Pekar, J. B. Lefton, C. McConville, J. Burleson, D. Sethio, E. Kraka, and T. Runčevski,
Cryst. Growth Des., 21, 1297-1306 (2021).
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- Describing Polytopal Rearrangement Processes of Octacoordinate Structures. I. Renewed Insights Into Fluxionality of Rhenium Polyhydride Complex ReH5(PPh3)2(pyridine),
Y. Tao, W. Zou, G.-G. Luo, and E. Kraka,
Inorg. Chem., 60, 2492-2502, (2021).
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- Exceptionally Long Covalent CC Bonds - A Local Vibrational Mode Study,
A. A. A. Delgado, A. Humason, R. Kalescky, M. Freindorf, and E, Kraka,
Molecules, 26, 950-1-950-25 (2021).
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- Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes,
N. Verma, Y. Tao, and E. Kraka,
J. Phys. Chem. B, 125, 2551- 2565 (2021).
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- Hydrogen Bonding in Natural and Unnatural Base Pairs - Explored with Vibrational Spectroscopy,
N. Beiranvand, M. Freindorf, and E. Kraka,
Molecules, 26, 2268-1-2268-22 (2021).
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- Intermolecular Interaction in 1- and 2-naphthol: A Rotational Spectroscopic and ab initio Study,
A. S. Hazrah, S. Nanayakkara, N. A. Seifert, E. Kraka, and W. Jaeger,
Phys. Chem. Chem. Phys., 24, 3722-3732 (2022).
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- Looking behind the scenes of Grubbs catalysis with the Unified Reaction Valley Approach (URVA),
M. Freindorf and E. Kraka,
in Chemical Reactivity Volume 1: Theories and Principles (S. Kaya, L. von Szentpály, G. Serdarolğu, and L. Guo, eds.), p. 3301 - 3324, Elsevier, Heidelberg, 2023.
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- Theoretical Insights into [NHC]Au(I) Catalyzed Hydroalkoxylation of Allenes: A Unified Reaction Valley Approach Study,
M. Makoś, M. Freindorf, Y. Tao, and E. Kraka,
J. Org. Chem., 86, 5714-5726 (2021).
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- Halogen Bonding Involving I2 and d8 Transition-Metal Pincer Complexes,
M. Freindorf, S. Yannacone, V. Oliveira, N. Verma, and E. Kraka,
Crystals, 11, 373-1-373-21 (2021).
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- Assessing the Intrinsic Strengths of Ion-Solvent and Solvent-Solvent Interactions for Hydrated Mg2+ Clusters,
A. A. A. Delgado, D. Sethio, and E. Kraka,
Inorganics, 9, 31-1-31-18 (2021).
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- Vibrational Analysis of Benziodoxoles and Benziodazolotetrazoles,
S. Yannacone, K. D. Sayala, M. Freindorf, N. V. Tsarevsky, and E. Kraka,
Physchem, 1, 45-68 (2021).
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- Generative adversarial networks for transition state geometry prediction,
M. Makoś, N. Verma, E. C. Larsson, M. Freindorf, and E. Kraka,
J. Chem. Phys., 155, 024116-1--024116-11 (2021).
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- Substituted hydrocarbon: a CCSD(T) and local vibrational mode investigation,
A. A. A. Delgado, D. Sethio, D. Matthews, V. P. Oliveira, and E. Kraka,
Mol. Phys., 21-22, e1970844, (2021).
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- Relating Bond Strength and Nature to the Thermodynamic Stability of Hypervalent Togni-Type Iodine Compounds,
V. P. Oliveira, B. L. Marcial, F. B. Machado, and E. Kraka,
ChemPlusChem, 86, 1199-1210 (2021).
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- Pancake bonding seen through the eyes of spectroscopy,
A. A. A. Delgado, A. Humason, and E. Kraka,
In Density Functional Theory - Recent Advances, New Perspectives and Applications, IntechOpen, 1-12 (2021).
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- Pivotal role of water molecules in the photodegradation of pymetrozine: New insights for developing green pesticides,
X. Liang, F. Guan, Z. Ling, H. Wang, Y. Tao, E. Kraka, H. Huang, C. Yu, D. Li, J. He, and H. Fang,
J. Hazardous Materials, 423, 127197-1-127197-10 (2022).
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- On the formation of CN bonds in Titan's atmosphere - a unified reaction valley approach study,
M. Freindorf, N. Beiranvand, A. A. A. Delgado, Y. Tao, and E. Kraka,
J. Mol. Model., 27, 320-1-320-20 (2021).
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- Analysis of spectator chemical bonds in SN2@C and @Si reaction mechanisms in the gas phase,
C. Vital dos Santos-Jr., M. A. F. de Souza, E. Kraka, and R. T. Moura Jr.,
Chem. Phys. Lett., 787, 139282-1-139282-7 (2022).
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- Unusual Intramolecular Motion of ReH92- in K2ReH9 Crystal: Circle Dance and Three-Arm Turnstile Mechanisms Revealed by Computational Studies,
Y. Tao, X. Wang, W. Zou, G.-G.Luo, and E. Kraka,
Inorg. Chem., 61, 1041-1050 (2021).
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- Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture,
S. Nanayakkara, Y. Tao, and E. Kraka,
J. Chem. Theory Comput., 18, 562-579 (2022).
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- Chemical Bonding in Homogenous Catalysis - Seen Through the Eyes of Vibrational Spectroscopy,
E. Kraka and M. Freindorf,
In Comprehensive Computational Chemistry, (ELS, MRW-CMPC@elsevier.com), Elsevier, p1-27, (2022).
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- A Closer Look at the Isomerization of 5-androstene-3,17-dione to 4-androstene-3,17-dione in Ketosteroid Isomerase,
M. Freindorf, Y. Tao, and E. Kraka,
J. Comput. Biophys. Chem., 21, 313-333 (2022).
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- LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis,
Y. Tao, W. Zou, S. Nanayakkara, and E. Kraka,
J. Chem. Theory Comput., 18, 1821-1837 (2022).
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- CO Bonding in Hexa- and Pentacoordinate Carboxy-Neuroglobin - A QM/MM and Local Vibrational Mode Study,
M. Freindorf, A. A. A. Delgado, and E. Kraka,
J. Comp. Chem., 43, 1725–1746 (2022).
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- Bonding in Nitrile Photo-dissociating Ruthenium Drug Candidates -- A Local Vibrational Mode Study,
M. McCutcheon, M. Freindorf, and E. Kraka,
J. Chem. Phys., 157, 014301-1--014301-15 (2022).
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- Uranium: The Nuclear Fuel Cycle and Beyond,
B. M. T. Costa Peluzo, and E. Kraka,
Int. J. Mol. Sci., 23, 4655-1-4655-19 (2022).
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- Theoretical insights into the linear relationship between pKa values and vibrational frequencies,
M. Quintano and E. Kraka,
Chem. Phys. Lett, 803, 139746-1-139746-7 (2022).
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- BF3-Catalyzed Diels-Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution-An URVA and Local Vibrational Mode Study,
M. Freindorf and E. Kraka,
Catalysts, 12, 415-1-415-26 (2022).
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- Allosteric control of ACE2 peptidase domain dynamics,
F. Trozzi, N. Karki, Z. Song, N. Verma, E. Kraka, B. Zoltowski, and P. Tao,
Org. Biomol. Chem., 20, 3605-3618 (2022).
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- Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols -- A combined URVA and Local Mode Study,
M. Freindorf and E. Kraka,
Catalysts, 12, 789-1--89-31 (2022).
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- Feature Article: The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena,
E. Kraka, M. Quintano, H. W. La Force, J. J. Antonio, and M. Freindorf,
J. Phys. Chem. A, 126, 8781−8798 (2022).
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- Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study,
A. Madushanka, N. Verma, M. Freindorf, and E.Kraka,
Int. J. Mol. Sci., 23, 12310-1-12310-25 (2022).
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- Dynamics of the Energy Transfer Process in Eu(III) Complexes Containing Polydentate Ligands Based on Pyridine, Quinoline, and Isoquinoline as Chromophoric Antennae,
A. N. C. Neto, R. T. Moura Jr., L. D. Carlos, O. L. Malta, M. Sanadar, A. Melchior, E. Kraka, S. Ruggieri, M. Bettinelli, and F. Piccinelli,
Inorg. Chem., 61, 16333-16346 (2022).
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- Exploring the frontiers of chemistry with a general reactive machine learning potential,
S. Zhang, M. Makoś, R. Jadrich, E. Kraka, K. Barros, B. Nebgen, S. Tretiak, O. Isayev, N. Lubbers, R. Messerly, and J. Smith,
ChemRxiv 1-18 (2022).
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- Featuring a new computational protocol for the estimation of intensity and overall quantum yield in lanthanide chelates with applications to Eu(III) mercapto-triazole Schiff base ligands,
R. Moura Jr., M. Quintano, C. Vital dos Santos-Jr., V. Albuquerque, E. Aguiar, E. Kraka, and A. Carniero Neto,
Optical Materials, X 16, 100216-1-100216-15 (2022).
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- Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems,
R. Moura Jr., M. Quintano, J. Antonio, and E. Kraka,
J. Phys. Chem. A, 126, 9313-9331 (2022).
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- URVA and Local Mode Analysis of an Iridium Pincer Complex Efficiently Catalyzing the Hydrogenation of Carbon Dioxide,
M. Freindorf and E. Kraka,
Inorganics, 10, 234-1--234-31 (2022).
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- Local mode analysis of characteristic vibrational coupling in nucleobases and Watson--Crick base pairs of DNA,
M. Quintano, A. A. A. Delgado, R. Moura Jr., M. Freindorf and E. Kraka,
Electron. Struct., 4, 044005-1-044005-16 (2022).
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- Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy,
M. Freindorf, M. McCutcheon, N. Beiranvand and E. Kraka,
Molecules, 28, 263-1-263-23 (2023).
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- Weak and strong π-interactions between two monomers - assessed with local vibrational mode theory,
W. Zou, M. Freindorf, V. Oliveira, Y. Tao and E. Kraka,
Can. J. Chem., 101, 615–632 (2023).
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- Reaction mechanism – explored with the unified reaction valley approach: Feature article,
E. Kraka, J. Antonio and M. Freindorf,
Chem. Commun., 59, 7151 – 7290 (2023).
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- Quantum Mechanical Assessment of Protein-Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory,
A. Madushanka, R. Moura Jr., N. Verma and E. Kraka,
Int. J. Mol. Sci., 24, 6311-1-6311-24 (2023).
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- The pKa rule in light of local mode force constants,
M. Quintano, R. Moura Jr., and E. Kraka,
Chem. Phys. Lett., 826, 140654–1–140654–7 (2023).
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- Non-covalent π-interactions in mutated aquomet-Myoglobin proteins: A QM/MM and Local Vibrational Mode Study,
J. Antonio and E. Kraka,
Biochemistry, 62, 2325-2337 (2023).
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- Linear versus Bent Uranium(II) Metallocenes - A Local Vibrational Mode Study,
B. Peluzo, M. Makoś, R. Moura Jr., M. Freindorf and E. Kraka,
Inorg. Chem., 62, 12510-12524 (2023).
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- Characterizing guanine’s binding modes with potential Ru(II) monofunctional adducts: A local vibrational mode study,
H. La Force and E. Kraka,
Chem. Phys. Lett., 828, 140733-1-140733-10 (2023).
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- XInsight: Revealing Model Insights for GNNs with Flow-Based Explanations,
E. Laird, A. Madushanka, E. Kraka and C. Clark,
Springer Nature Switzerland, p. 303-320 (2023).
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- Hydrogen Sulfide Ligation in Hemoglobin I of Lucina pectinata - A QM/MM and Local Mode Study,
M. Freindorf, J. Antonio and E. Kraka,
J. Phys. Chem. A, 127, 8316-832 (2023).
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- Iron-histidine bonding in bishistidyl hemoproteins - A local vibrational mode study,
M. Freindorf, J. Antonio and E. Kraka,
J. Comput. Chem., DOI: 10.1002/jcc.27267 (2023).
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- Chemical Bonding in Uranium-based Materials: A Local Vibrational Mode Case Study of Cs2UO2Cl4 and UCl4 Crystals,
F. Bodo, A. Erba, E. Kraka and R. Moura Jr.,
J. Comput. Chem., in press (2023).
- Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study,
Y. Dangat, M. Freindorf and E. Kraka,
J. Am. Chem. Soc., DOI: https://doi.org/10.1021/jacs.3c06397 (2023).
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- Unraveling the effect of aromaticity for the dynamics of excited states of single benzene fluorophores,
M. Filatov(Gulak), V. Mironov and E. Kraka,
J. Comput. Chem., in press (2023).
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