publication record


Paz, Nieves R.; Rodriguez-Sosa, Dionisio; Valdes, Haydee; Marticorena, Ricardo; Melian, Daniel; Belen Copano, M.; Gonzalez, Concepcion C.; Herrera, Antonio J.
Chemoselective Intramolecular Functionalization of Methyl Groups in Nonconstrained Molecules Promoted by N-Iodosulfonamides
Organic Letters 2015, 17, 2370-2373


Diaz, Natalia; Suarez, Dimas and Valdes, Haydee
Unravelling the molecular structure of the catalytic domain of Metalloproteinase-2 in complex with a triple-helical peptide by means of molecular dynamic simulations
Biochemistry 2013, 52, 8556-8569


Suarez, Dimas; Rayon, Victor M.; Diaz, Natalia and Valdes, Haydee
Ab Initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies
J. Phys. Chem. A 2011, 115, 11331-11343


Valdes, Haydee; Diaz, Natalia; Suarez, Dimas and Fernandez-Recio, Juan
Interdomain conformations in the full-length MMP-2 enzyme explored by protein-protein docking calculations using pyDock
J. Chem. Theory Comput. 2010, 6, 2204-2213

Gloaguen, Eric; Valdes, Haydee; Pagliarulo, Francesca; Pollet, Rodolphe; Tardivel, Benjamin; Hobza, Pavel; Piuzzi, Francois and Mons, Michel
Experimental and theoretical investigation of the aromatic-aromatic interaction in isolated capped dipeptides
J. Phys. Chem. A 2010, 114, 2973-2982

Bisogno, Fabricio R.; Garcia-Urdiales, Eduardo; Valdes, Haydee; Lavandera, Ivan; Kroutil, Wolfgang; Suarez, Dimas and Gotor, Vicente
Ketone-alcohol hydrogen-transfer equilibria: is the biooxidation of halohydrins blocked?
Chem. Eur. J. 2010, 16, 11012-11019


Valdes, Haydee; Pluhackova, Kristyna and Hobza, Pavel
Phenylalanyl-glycyl-phenylalanine tripeptide: A model system for aromatic-aromatic side chain interactions in proteins
J. Chem. Theory Comput. 2009, 5, 2248-2256

Rayon, Victor M.; Redondo, Pilar; Valdes, Haydee; Barrientos, Carmen and Largo, Antonio
Polyisocyanides of titanium
J. Phys. Chem. A 2009, 113, 1574-1577


Diaz, Natalia; Suarez, Dimas and Valdes, Haydee
From the X-ray compact structure to the elongated form of the full-length MMP-2 enzyme in solution: A molecular dynamics study
J. Am. Chem. Soc. 2008, 130, 14070-14071

Valdes, Haydee; Klusak, Vojtech; Pitonak, Michal; Exner, Otto; Stary, Ivo; Hobza, Pavel and Rulisek, Lubomir
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]Helicenes and Phe-Gly-Phe tripeptide
J. Comput. Chem. 2008, 29, 861-870

Rayon, Victor M.; Valdes, Haydee; Diaz, Natalia and Suarez, Dimas
Monoligand Zn(II) complexes: Ab initio benchmark calculations and comparison with density functional theory methodologies
J. Chem. Theory Comput. 2008, 4, 243-256

Valdes, Haydee; Spiwok, Vojtech; Rezac, Jan; Reha, David; Abo-Riziq, Ali G.; de Vries, Mattanjah S. and Hobza, Pavel
Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: Experiment and Theory
Chem. Eur. J. 2008, 14, 4886-4898

Rezac, Jan; Jurecka, Petr; Riley, Kevin E.; Cerny, Jiri; Valdes, Haydee; Pluhackova, Kristyna; Berka, Karel; Rezac, Tomas; Pitonak, Michal; Vondrasek, Jiri and Hobza, Pavel
Quantum Chemistry benchmark energy and geometry database for molecular clusters and complex molecular systems ( A users manual and examples
Collect. Czech. Chem. Commun. 2008, 73, 1261-1270

Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan and Hobza, Pavel
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force fields
Phys. Chem. Chem. Phys. 2008, 10, 2747-2757

Callahan, Michael P.; Gengeliczki, Zsolt; Svadlenak, Nathan; Valdes, Haydee; Hobza, Pavel and de Vries, Mattanjah S.
Non-standard base pairing and stacked structures in methyl xanthine clusters
Phys. Chem. Chem. Phys. 2008, 10, 2819-2826


Redondo, Pilar; Rayon, Victor M.; Valdes, Haydee; Barrientos, Carmen and Largo, Antonio
A theoretical study of the [FeCN]+ system: Cyanide-isocyanide competition and isomerization barrier
Chem. Phys. Lett. 2007, 445, 22-27

Rayon, Victor M.; Redondo, Pilar; Valdes, Haydee; Barrientos, Carmen and Largo, Antonio
Cyanides and isocyanides of first-row transition metals: Molecular structure, bonding, and isomerization barriers
J. Phys. Chem. A 2007, 111, 6334-6344

Kubar, Tomas; Jurecka, Petr; Cerny, Jiri; Rezac, Jan; Otyepka, Michal; Valdes, Haydee and Hobza, Pavel
Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems
J. Phys. Chem. A 2007, 111, 5642-5647

Cerny, Jiri; Jurecka, Petr; Hobza, Pavel and Valdes, Haydee
Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): A promising tool for studying isolated small peptides,
J. Phys. Chem. A 2007, 111, 1146-1154

Kabelac, Martin; Valdes, Haydee; Sherer, Edward C.; Cramer, Christopher J. and Hobza, Pavel
Benchmark RI-MP2 database of nucleic acid base trimers: performance of different density functional models for prediction of structures and binding energies,
Phys. Chem. Chem. Phys. 2007, 9, 5000-5008


Parreira, Renato L. T.; Valdes, Haydee and Galembeck, Sergio E.
Computational study of formamide-water complexes using the SAPT and AIM methods
Chem. Phys. 2006, 331, 96-110

Valdes, Haydee; Reha, David and Hobza, Pavel
Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: Ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations
J. Phys. Chem. B 2006, 110, 6385-6396


Reha, David; Valdes, Haydee; Vondrasek, Jiri; Hobza, Pavel; Abu-Riziq, Ali; Crews, Bridgit and de Vries, Mattanjah S
Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic Simulations
Chem. Eur. J. 2005, 11, 6803-6817

Dabkowska, Iwona; Gonzalez, Haydee Valdes; Jurecka, Petr and Hobza, Pavel
Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5′-d(GCGAAGC)-3′ hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels
J. Phys. Chem. A 2005, 109, 1131-1136


Valdes, Haydee and Sordo, Jose A
The OCS·(HCCH)2 van der Waals complex: ab initio predictions for the geometry and dynamics
Chem. Phys. Lett. 2004, 387, 428-432

Valdes, Haydee and Sordo, Jose A
The N2O·N2O, N2O·SO2, and (N2O)2·SO2 van der Waals complexes: An ab initio theoretical analysis
J. Phys. Chem. A 2004, 108, 2062-2071

Pittner, Jiri; Gonzalez, Haydee Valdes; Gdanitz, Robert J and Carsky, Petr
The performance of the multireference Brillouin-Wigner coupled cluster singles and doubles method on the insertion of Be into H2,
Chem. Phys. Lett. 2004, 386, 211-215


Valdes, Haydee and Sordo, Jose A
(OCS)3 van der Waals complex: A theoretical study
J. Phys. Chem. A 2003, 107, 7845-7851

Valdes, Haydee and Sordo, Jose A
A theoretical analysis of the weakly bound complexes H3P···XY (XY = HBr, HCl, Br2, BrCl), H3N·BrCl
Chem. Phys. Lett. 2003, 371, 386-393

Valdes, Haydee and Sordo, Jose A
Trimethylene sulfide center dot center dot center dot (HCl)n (n=1, 2) complexes: A theoretical study,
J. OF Phys. Chem. A, 2003, 107, 899-907


Valdes, Haydee and Sordo, Jose A
Ab initio study on the (OCS)2·CO2 van der Waals trimers,
J. OF Phys. Chem. A, 2002, 106, 3690-3701

Valdes, Haydee and Sordo, Jose A
Ab initio and DFT studies on van der Waals trimers: The OCS·(CO2)2 complexes,
J. Comput. Chem. 2002, 23, 444-455


Valdes, Haydee; Rayon, Victor M and Sordo, Jose A
High-level ab initio predictions of CO2·N2O structure,
Int. J. Quantum Chem. 2001, 84, 78-85

Valdes, Haydee and Sordo, Jose A
The pentamethylene sulfide·HCl dimer: a theoretical study
Chem. Phys. Lett. 2001, 333, 169-180


Valdes, Haydee; Rayon, Victor M and Sordo, Jose A
The tetrahydropyran·HCl dimer: a theoretical study,
Chem. Phys. Lett. 2000, 320, 507-512


Valdes, Haydee; Rayon, Victor M and Sordo, Jose A
On the violation of Legon-Millen’s rules for predicting angular geometries of hydrogen-bonded dimers: an ab initio study,
Chem. Phys. Lett. 1999, 309, 265-273

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