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Published Papers

  1. Gündoğdu, Ö., Atalay, A., Turhan, P., Anıl, B., Şahin, E., Bozkaya, U., Kishalı, N. H., Kara, Y.  2024. "Reduction of 2-phenyl-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione with NaBH4: Investigation of Exo-selectivity and Reaction Mechanism via Theoretical Computations", J. Mol. Struct., 1319, 139520. DOI: 10.1016/j.molstruc.2024.139520.

  2. Behnle, S., Richter, R., Völkl, L., Idzko, P., Förstner, A., Bozkaya, U., Fink, R. F. 2022. "Accurate Property Prediction by Second Order Perturbation Theory: The REMP and OO-REMP Hybrids", J. Chem. Phys., 157, 104111. DOI: 10.1063/5.0105628

  3. Bozkaya, U., Ermiş, B. 2022. "Linear-Scaling Systematic Molecular Fragmentation Approach for Perturbation Theory and Coupled-Cluster Methods", J. Chem. Theory Comput. 18, 9, 5349–5359. DOI: 10.1021/acs.jctc.2c00587

  4. Altaş, A., Gültekin, D. D., Acar, M., Cücü, E., Karatay, A., Elmalı, A., Atalay, A., Demircan, Ç. A., Bozkaya, U., Kazaz, C., Şahin, E., Bozdemir, Ö. A. 2022. "Bay- and Peri-functionalized Donor-acceptor Perylene Monoimides via Nitration and Nucleophilic Substitution/reduction Pathway". Mater. Today Chem., 24, 100908. DOI: 10.1016/j.mtchem.2022.100908

  5. Gündoğdu, Ö., Atalay, A., Çelebioğlu, N., Anıl, B., Şahin, E., Şanlı-Mohamed, G., Bozkaya, U., Kara, Y. 2022. "Regio- and Stereo-chemical Ring-opening Reactions of the 2,3-epoxy alcohol Derivative with Nucleophiles: Explanation of the Structures and C-2 Selectivity Supported by Theoretical Computations", J. Mol. Struct., 1264, 133163. DOI: 10.1016/j.molstruc.2022.133163

  6. Ünal, A., Bozkaya, U. 2022. "Efficient Implementation of Equation-of-Motion Coupled-Cluster Singles and Doubles Method with the Density-Fitting Approximation: An Enhanced Algorithm for the Particle−Particle Ladder Term". J. Chem. Theory Comput., 18, 1489-1500. DOI:10.1021/acs.jctc.1c01000

  7. Bozkaya, U., Ermiş, B., Alagöz, Y., Ünal, A., Uyar, A. K. 2022. "MacroQC 1.0: An Electronic Structure Theory Software for Large-Scale Applications". J. Chem. Phys., 156, 044801. DOI: 10.1063/5.0077823.

  8. Polat, İ., Eşsiz, S., Bozkaya, U., Salamci, E. 2022. "Efficient and Regioselective Synthesis of Dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and Its Bicyclic Derivatives", Beilstein J. Org. Chem., 18, 77–85. DOI: 10.3762/bjoc.18.7

  9. Ermiş, B., Ekinci, E., Bozkaya, U. 2021. "State-Of-The-Art Computations of Vertical Electron Affinities with the Extended Koopmans’ Theorem Integrated with the CCSD(T) Method", J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.1c00938

  10. Eşsiz, S., Bozkaya, U. 2021. "A Computational Study for the Reaction Mechanism of 2, 2-azobis (isobutyronitrile)-initiated Oxidative Cleavage of the Geminal Alkenes", Org. Biomol. Chem.,19, 9483–9490, DOI: 10.1039/d1ob01607e.

  11. Alagöz, Y., Ünal, A., Bozkaya, U. 2021. “Efficient Implementations of the Symmetric and Asymmetric Triple Excitation Corrections for the Orbital-Optimized Coupled-Cluster Doubles Method with the Density-Fitting Approximation”, J. Chem. Phys., 155, 114104. DOI: 10.1063/5.0061351.

  12. Ermiş, B., Ünal, A., Soydaş, E., Bozkaya, U. 2021. "Anharmonic Force Field from Coupled-Cluster Methods and Accurate Computation of Infrared Spectra",  Adv. Quantum Chem.,  83, 139-153. DOI: 10.1016/bs.aiq.2021.05.003.

  13. Bozkaya, U. 2021. "Molint 1.0: A Framework for the Computation of Molecular Integrals and Their Derivatives for Density-fitted Methods", Int. J. Quantum Chem., 121, e26623. DOI: 10.1002/qua.26623

  14. Bozkaya, U., Ünal, A., Alagöz, Y. 2020. “Energy and Analytic Gradients for the Orbital-Optimized Coupled-Cluster Doubles Method with the Density-Fitting Approximation: An Efficient Implementation”, J. Chem. Phys., 153, 244115. DOI: 10.1063/5.0035811

  15. Mammadova, F., Hamarat, B., Ahmadli, D., Şahin, O., Bozkaya, U., Türkmen, Y. E. 2020. "Polarization‐Enhanced Hydrogen Bonding in 1,8‐Dihydroxynaphthalene: Conformational Analysis, Binding Studies and Hydrogen Bonding Catalysis", ChemistrySelect, 5, 13387–13396. DOI: 10.1002/slct.202002960

  16. Servan, S. A., Ünal, A., Hamarat, B., Bozkaya, U. 2020. "Assessment of the Density-Fitted Second-Order Quasidegenerate Perturbation Theory for Transition Energies: Accurate Computations of Singlet-Triplet Gaps for Charge-Transfer Compounds", J. Phys. Chem. A, 124, 6889–6898. DOI: 10.1021/acs.jpca.0c04555

  17. Eşsiz, S., Bozkaya, U. 2020. "Computational Study for the Reaction Mechanism of N-Hydroxyphthalimide-Catalyzed Oxidative Cleavage of Alkenes", J. Org. Chem., 85, 10136–10142. DOI: 10.1021/acs.joc.0c01472

  18. Smith, D. G. A., Burns, L. A., Simmonett, A. C., Parrish, R. M., Schieber, M. C., Galvelis, R., Kraus, P., Kruse H., Remigio, R. D., Alenaizan, A.,  James, A. M., Lehtola, S., Misiewicz, J. P., Scheurer, M., Shaw, R. A., Schriber, J. B., Xie, Y., Glick, Z. L., Sirianni, D. A., O’Brien, J. S., Waldrop, J. M., Kumar, A., Hohenstein, E. G., Pritchard, B. P., Brooks, B. R., Schaefer III, H. F., Sokolov, A. Y., Patkowski, K., DePrince III, A. E., Bozkaya, U., King, R. A, Evangelista, F. A., Turney, J. M., Crawford, T. D., Sherrill, C. D. 2020. "Psi4 1.4: Open-source software for high-throughput quantum chemistry", J. Chem. Phys., 152, 184108. DOI: 10.1063/5.0006002

  19. Warden, C. E., Smith, D. G. A., Burns, L. A., Bozkaya, U., Sherrill, C. D. 2020. "Efficient and automated computation of accurate molecular geometries using focal-point approximations to large-basis coupled-cluster theory". J. Chem. Phys., 152, 124109. DOI: 10.1063/5.0004863

  20. Ünal, A., Bozkaya, U. 2020. " Ionized water clusters (H2O)+n, n= 2 to 6: A high-accuracy study of structures and energetics". Int. J. Quantum Chem., 120, e26100. DOI: 10.1002/qua.26100.

  21. Atakay, M., Aksakal, F., Bozkaya, U., Salih, B., Wesdemiotis, C. 2020. "Conformational Characterization of Polyelectrolyte Oligomers and Their Noncovalent Complexes Using Ion Mobility-Mass Spectrometry", J. Am. Soc. Mass Spectrom., 31, 441−449. DOI: 10.1021/jasms.9b00135

  22. Bozkaya, U., Soydaş, E., Filiz, B. 2020. "State-of-the-Art Computations of Dipole Moments Using Analytic Gradients of High-Level Density-Fitted Coupled-Cluster Methods with Focal-Point Approximations". J. Comput. Chem., 41, 769–779. DOI: 10.1002/jcc.26126 

  23. Bozkaya, U. 2019. "An Efficient Implementation of the Second-Order Quasidegenerate Perturbation Theory with Density-Fitting and Cholesky Decomposition Approximations: Is It Possible to Use HartreeFock Orbitals for a Multiconfigurational Perturbation Theory?". J. Chem. Theory Comput., 15 (8), 4415-4429. DOI: 10.1021/acs.jctc.9b00378

  24. Köse, A., Ünal A., Şahin, E., Bozkaya U., Kara Y. 2019. “An anomalous addition of chlorosulfonyl isocyanate to a carbonyl group: the synthesis of ((3aS,7aR,E)-2-ethyl3-oxo-2,3,3a,4,7,7a-hexahydro-1H-isoindol1-ylidene)sulfamoyl chloride”. Beilstein J. Org. Chem., 15, 931–936. DOI:10.3762/bjoc.15.89

  25. Donmez, S. E., Soydaş, E., Aydın, G., Şahin, O., Bozkaya, U. and Türkmen, Y. E. 2019. “Aza-Nazarov Cyclization Reactions via Anion Exchange Catalysis”. Org. Lett., 21 (2), 554-558. DOI: 10.1021/acs.orglett.8b03886

  26. Bozkaya, U., Ünal, A. 2018. "State-of-the-Art Computations of Vertical Ionization Potentials with the Extended Koopmans’ Theorem Integrated with the CCSD(T) Method". J. Phys. Chem. A, 122, 4375−4380. DOI: 10.1021/acs.jpca.8b01851

  27. Ünal, A., Bozkaya, U. 2018. "Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics". J. Chem. Phys., 148, 124307, DOI: 10.1063/1.5025233

  28. Bozkaya, U. 2018. "Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation". J. Comput. Chem., 39, 351–360. DOI: 10.1002/jcc.25122

  29. Demircan, Ç. A., Bozkaya, U. 2017. "Transition Metal Cation−π Interactions: Complexes Formed by Fe2+ , Co2+, Ni2+, Cu2+, and Zn2+ Binding with Benzene Molecules". J. Phys. Chem. A, 121(34), pp 6500–6509. DOI: 10.1021/acs.jpca.7b05759

  30. Koçak, R., Yıldız, D., Bozkaya, U., Daştan, A., Bozdemir, Ö. A. 2017. "Dihydropyridazine-appended dibenzosuberenones as a new class of fluorophores: Application to fluoride sensing". Tett. lett., Volume 58, Issue 30, 2981-2985. DOI: 10.1016/j.tetlet.2017.06.059

  31. Bozkaya, U., Sherrill, C. D. 2017. "Analytic energy gradients for the coupled-cluster singles and doubles with perturbative triples method with the density-fitting approximation". J. Chem. Phys.,  147, 044104. DOI: 10.1063/1.4994918

  32. Parrish, R. M., Burns, L. A., Smith, D. G. A., Simmonett, A. C., De Prince, III, A. E., Hohenstein, E. G., Bozkaya, U., Sokolov, A. Y., Remigio, R. D., Richard, R. M., Gonthier, J. F., James, A. M., McAlexander, H. R., Kumar, A., Saitow, M., Wang, X., Pritchard, B. P., Verma, P., Schaefer, III, H. F., Patkowski, K., King, R. A., Valeev, E. F., Evangelista, F. A., Turney, J. M., Crawford, T. D. and Sherrill, C. D. 2017. "PSI4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability". J. Chem. Theory Comput., 13 (7), 3185–3197. DOI: 10.1021/acs.jctc.7b00174

  33. Bozkaya, U. 2016. “Orbital-Optimized MP3 and MP2.5 with Density-Fitting and Cholesky Decomposition Approximations”. J. Chem. Theory Comput., 12, 1179-1188. DOI: 10.1021/acs.jctc.5b01128

  34. Bozkaya, U. 2016. “Orbital-Optimized Linearized Coupled-Cluster Doubles with Density- Fitting and Cholesky Decomposition Approximations: An Efficient Implementation”. Phys. Chem. Chem. Phys., 18, 11362-11373. DOI: 10.1039/C6CP00164E

  35. Bozkaya, U. 2016. “A Noniterative Asymmetric Triple Excitation Correction for The Density-Fitted Coupled-Cluster Singles and Doubles Method: Preliminary Applications”. J. Chem. Phys., 144, 144108. DOI: 10.1063/1.4945706.

  36. Bozkaya, U., Sherrill, C. D. 2016. “Analytic Energy Gradients for the Coupled-Cluster Singles and Doubles Method with the Density-Fitting Approximation”. J. Chem. Phys., 144, 174103. DOI: 10.1063/1.4948318.

  37. Karaca, E.; Can, K. H.; Bozkaya, U.; Pekmez, N. Ö. 2016. “Charge Transfer Complex of p-aminodiphenyldiamine with Maleic Anhydride: spectroscopic, electrochemical and physical properties”. ChemPhysChem., 17, 2056-2065. DOI: 10.1002/cphc.201600161

  38. Yıldız, D.; Bozkaya, U. 2016. “Assessment of the Extended Koopmans’ Theorem for the Chemical Reactivity: Accurate Computations of Chemical Potentials, Chemical Hardnesses, and Electrophilicity Indices”. J. Comput. Chem., 37, 345-353. DOI: 10.1002/jcc.24225

  39. Üçüncü, M., Cantürk, C., Karakus, E., Zeybek, H., Bozkaya, U., Soydas, E., Sahin, E., Emrullahoğlu, M. 2016. "A Rare γ-Pyranopyrazole Skeleton: Design, One-Pot Synthesis and Computational study”. Org. Biomol. Chem., 14, 7490-7494. DOI: 10.1039/C6OB01099G

  40. Soydaş, E., Bozkaya, U. 2015. “Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions”. J. Chem. Theory Comput., 11, 1564−1573. DOI: 10.1021/ct501184w

  41. Bozkaya, U. 2014. “Derivation of General Analytic Gradient Expressions for Density-Fitted Post-Hartree-Fock Methods: An Efficient Implementation for the Density-Fitted Second-Order Møller-Plesset Perturbation Theory”. J. Chem. Phys., 141, 124108. DOI: 10.1063/1.4903269

  42. Bozkaya, U. 2014. “Analytic Energy Gradients and Spin Multiplicities for Orbital-Optimized Second-Order Perturbation Theory with Density-Fitting Approximation: An Efficient Implementation”. J. Chem. Theory Comput., 10, 4389-4399. DOI: 10.1021/ct500634s

  43. Bozkaya, U. 2014. “Orbital-Optimized Second-Order Perturbation Theory with Density-Fitting and Cholesky Decomposition Approximations: An Efficient Implementation”. J. Chem. Theory Comput.,10, 2371-2378. DOI: 10.1021/ct500231c

  44. Bozkaya, U. 2014. “Accurate Electron Affinities from the Extended Koopmans’ Theorem Based on Orbital-Optimized Methods”.  J. Chem. Theory Comput., 10, 2041-2048. DOI: 10.1021/ct500186j

  45. Soydaş, E., Bozkaya, U. 2014. “Assessment of the Orbital-Optimized Coupled-Electron Pair Theory for Thermochemistry and Kinetics: Improving upon CCSD and CEPA(1)”. J. Comput. Chem., 35 , 1073-1081. DOI: 10.1002/jcc.23592

  46. Bozkaya, U., Sherrill, C. D. 2014. “Orbital-optimized MP2.5 and Its Analytic Gradients: Approaching CCSD(T) Quality for Noncovalent Interactions”. J. Chem. Phys., 141, 204105. DOI: 10.1063/1.4902226.

  47. Soydaş, E.; Bozkaya, U. 2013. “Accurate Open-Shell Noncovalent Interaction Energies from the Orbital-Optimized Møller–Plesset Perturbation Theory: Achieving CCSD Quality at the MP2 Level by Orbital Optimization”. J. Chem. Theory Comput., 9, 4679-4683.  DOI: 10.1021/ct4008124

  48. Bozkaya, U. 2013. “The Extended Koopmans’ Theorem for Orbital-Optimized Methods: Accurate Computation of Ionization Potentials”. J. Chem. Phys., 139, 154105. DOI: 10.1063/1.4825041

  49. Bozkaya, U. 2013. “Analytic Energy Gradients for the Orbital-Optimized Third-Order Møller–Plesset Perturbation Theory”. J. Chem. Phys., 139, 104116.  DOI: 10.1063/1.4820877

  50. Bozkaya, U., Sherrill, C. D. 2013. “Orbital-Optimized Coupled-Electron Pair Theory and its Analytic Gradients: Accurate Equilibrium Geometries, Harmonic Vibrational Frequencies, and Hydrogen Transfer Reactions”. J. Chem. Phys., 139, 054104. DOI: 10.1063/1.4816628.

  51. Bozkaya, U., Sherrill, C. D. 2013. “Analytic Energy Gradients for the Orbital-Optimized Second-Order Møller–Plesset Perturbation Theory”. J. Chem. Phys., 138, 184103. DOI: 10.1063/1.4803662.

  52. Soydaş, E., Bozkaya, U. 2013. “Assessment of Orbital-Optimized Third-Order Møller-Plesset Perturbation Theory and Its Spin-Component and Spin-Opposite Scaled Variants for Thermochemistry and Kinetics”. J. Chem. Theory Comput., 9, 1452-1460. DOI: 10.1021/ct301078q

  53. Baglan, M., Ozturk, S., Gür, B., Meral, K., Bozkaya, U., Bozdemir, O. A., Atılgan, S. 2013. "Novel Phenomena for Aggregation Induced Emission Enhancement: Highly Fluorescent Hydrophobic TPE-BODIPY Couples in both Organic and Aqueous Media”. RSC Advances, 3, 15866-15874. DOI: 10.1039/C3RA40791H

  54. Bozkaya, U., Schaefer, H. F. 2012 “Symmetric and Asymmetric Triple-Excitation Corrections for Orbital-Optimized Coupled-Cluster Doubles Method: Improving Upon CCSD(T) and CCSD(T)Λ. Application to Potential Energy Surfaces”. J. Chem. Phys., 136, 204114.  DOI: 10.1063/1.4720382 

  55. Bozkaya, U., Turney, J. M., Yamaguchi, Y., Schaefer, H. F. 2012. “The Lowest-Lying Electronic Singlet and Triplet Potential Energy Surfaces for the HNO-NOH System: Energetics, Unimolecular Rate Constants, Tunneling and Kinetic Isotope Effects for the Isomerization and Dissociation Reactions”.  J. Chem. Phys., 136, 164303. DOI:10.1063/1.4704895.

  56. Metin, Ö., Alp, N., Akbayrak, S., Biçer, A., Gültekin, M. S., Özkar, S., Bozkaya, U. 2012. “Dihydroxylation of Olefins Catalyzed by Zeolite-Confined Osmium Nanoclusters: A Novel, Efficient, Reusable and Eco-Friendly Method for the Preparation of 1,2-cis-Diols”. Green Chem., 14, 1488-1492. DOI: 10.1039/C2GC16616J

  57. Bozkaya, U., Özkan, İ. 2012. “Thermal Denitrogenation of 7-isopropylidene-2,3-diaza-norbornene: Formation of Substituted 3-methylene-(1,4)-pentadienes”. Phys. Chem. Chem Phys., 14, 14282-14292. DOI: 10.1039/C2CP42349A

  58. Bozkaya, U., Özkan, İ. 2012. “Thermal Aromatizations of 2-Vinylmethylenecyclopropane and 3-Vinylcyclobutene”. J. Org. Chem., 77, 5714-5723. DOI: 10.1021/jo300877w

  59. Bozkaya, U., Özkan, İ. 2012. “Thermal Rearrangements of 1-Ethynyl-2-methylcyclopropane: A Computational Study”. J. Phys. Chem. A, 116, 3274-3281. DOI: 10.1021/jp3000575

  60. Bozkaya, U., Özkan, İ. 2012. “Potential Energy Surfaces for Rearrangements of Berson Trimethylenemethanes”. J. Phys. Chem. A, 116, 2309-2321. DOI: 10.1021/jp211518f

  61. Bozkaya, U., Özkan, İ. 2012. “Theoretical Study of Thermal Rearrangements of 1-Hexen-5-yne, 1,2,5-Hexatriene, and 2-Methylenebicyclo[2.1.0]pentane”. J. Org. Chem., 77, 2337-2344. DOI: 10.1021/jo202645k

  62. Bozkaya, U. 2011. “Orbital-Optimized Third-Order Møller-Plesset Perturbation Theory and Its Spin-Component and Spin-Opposite Scaled Variants: Application to Symmetry Breaking Problems”. J. Chem. Phys., 135, 224103. DOI: 10.1063/1.3665134

  63. Bozkaya, U., Turney, J. M., Yamaguchi, Y., Schaefer, H. F., Sherrill, C. D. 2011. “Quadratically Convergent Algorithm for Orbital Optimization in the Orbital-Optimized Coupled-Cluster Doubles Method and in Orbital-Optimized Second-Order Møller-Plesset Perturbation Theory”. J. Chem. Phys., 135, 104103. DOI: 10.1063/1.3631129.

  64. Bozkaya, U., Schaefer, H. F. 2010. “The Ten Chemically Transparent Dinitro-Naphtalene Isomers and their Radical Anions”. Mol. Phys., 108, 2491. DOI: 10.1080/00268976.2010.507225

  65. Bozkaya, U., Turney, J. M., Yamaguchi, Y., Schaefer, H. F. 2010. “The Barrier Height, Unimolecular Rate Constant, and Lifetime for the Dissociation of HN2”. J. Chem. Phys., 132, 064308. DOI:10.1063/1.3310285             

  66. Çaykara, T., Bozkaya, U., Kantoğlu, Ö. 2003. “Network Structure and Swelling Behavior of Poly(acrylamide/crotonic acid) Hydrogels in Aqueous Salt Solutions”. J. Polym. Sci. Part B: Polym. Phys., 41, 1656. DOI: 10.1002/polb.10500

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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