Publications
Our Publications
Publications at NJIT
2024
(50) Shi, Y.; Shakib, F. A. "Machine learning committee neural network potential energy surfaces for two-dimensional metal-organic frameworks" ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-9hmsb.
(49) Zhang, Z.; Shi, Y.; Shakib, F. A. "Machine learning prediction of thermodynamic stability and electronic properties of 2D layered conductive metal-organic frameworks", ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-0mkw8.
(48) London, N.; Limbu, D.K.; Momeni, M.R.; Shakib, F.A. “DL_POLY Quantum v2.0: A modular general-purpose software for advanced path integral simulations", J. Chem. Phys. 2024, 160, 132501. (preprint)
(47) Limbu, D.K.; Shakib, F.A. “SHARP pack: A modular software for incorporating nuclear quantum effects into non-adiabatic quantum dynamic simulations in condensed phases", Software Impacts, 2024, 19, 100604.
2023
(46) Limbu, D.K.; Shakib, F.A. “Frustrated hops in Ring Polymer Surface Hopping: Real-time dynamics and detailed balance", J. Phys. Chem. Lett. 2023, 14, 8658. (preprint)
(45) Shi, Y.; Limbu, D.K.; Zhang, Z.; Momeni, M.R.; Shakib, F.A. “Effects of Defects and Presence of Open-Metal Sites on the Structure and Dynamics of Water in Hydrophobic Zeolitic Imidazolate Frameworks", J. Chem. Inf. Model. 2023, 63, 7097-7106.
(44) Zhang, Z.; Valente, D.; Shi, Y.; Limbu, D.K.; Momeni, M.R.; Shakib, F.A. “In Silico High-Throughput Design and Prediction of Structural and Electronic Properties of Low-Dimensional Metal-Organic Frameworks”, ACS Appl. Mater. Interfaces, 2023, 15, 9494. (preprint)
2022
(43) Shi, Y.; Momeni, M.R.; Chen, Y-.J.; Limbu, D.K.; Zhang, Z.; Shakib, F.A. “Water Induced Structural Transformations in Flexible 2D Layered Conductive Metal-Organic Frameworks”, Chem. Mater. 2022, 34, 7730.
(42) Dell'Angelo, D.; Momeni, M.R.; Pearson, S.; Shakib, F.A. "Modeling energy transfer and absorption spectra in layered metal-organic frameworks based on a Frenkel-Holstein Hamiltonian" J. Chem. Phys. 2022, 156, 044109. (preprint)
2021
(41) Dell'Angelo, D.; Brown, S.E.; Momeni, M.R.; Shakib, F.A. "Downscaling an open quantum system: an atomistic approach applied to photovoltaics". In Green Chemistry and Computational Chemistry, 1st ed; Mammino, L; Elsevier, 2021.
(40) Zhang, Z.; Dell'Angelo, D.; Momeni, M.R.; Shi, Y.; Shakib, F.A. "Metal-to-semiconductor transition in two-dimensional metal-organic frameworks: An ab initio dynamics perspective" ACS Appl. Mater. Interfaces 2021, 13, 25270.
(39) Momeni, M.R.; Zhang, Z.; Dell'Angelo, D.; Shakib, F.A. "Tuning Electronic Properties of Conductive 2D Layered Metal-Organic Frameworks via Host-Guest Interactions: Dioxygen as An Electroactive Chemical Stimuli", APL Mater. 2021, 9, 051109. (2D Materials Special Collection)
(38) Brown, S.E.; Shakib, F.A. “Recent Progress in Approximate Quantum Dynamics Methods for the Study of Proton-Coupled Electron Transfer Reactions”, Phys. Chem. Chem. Phys. 2021, 23, 2535-2556. (Invited Perspective, Inside front cover)
(37) Momeni, M.R.; Zhang, Z.; Dell'Angelo, D.; Shakib, F.A. “Gauging van der Waals Interactions in Aqueous Solutions of 2D MOFs: When Water Likes Organic Linkers More than Open-metal Sites”, Phys. Chem. Chem. Phys. 2021, 23, 3135-3143.
(36) Momeni, M.R.; Zhang, Z.; Shakib, F.A. “Deterministic Role of Structural Flexibility on Catalytic Activity of Conductive 2D Layered Metal-Organic Frameworks”, Chem. Commun. 2021, 57, 315-318. (Front cover)
2020
(35) Lee, H.; Shakib, F.A.; Liu, K.; Liu, B.; Bubach, B.; Varma, R.S.; Jang, H.W.; Shokouhimehr, M.; Ostadhassan, M. “Adsorption based realistic molecular model of amorphous kerogen”, RSC Adv., 2020,10, 23312.
2019
(34) Lee, H.; Ostadhassan, M.; Shakib, F.A.; Shokouhimehr, M.; Bubach, B.; Kong, L. “Optimal Separation of CO2/CH4/Brine with Amorphous Kerogen: A Thermodynamics and Kinetics Study”, J. Phys. Chem. C, 2019, 123, 20877.
Publications Prior to NJIT
(33) Mandal, A.; Sandoval J.S.; Shakib, F.A.; Huo, P. “Direct Simulation of Proton-Coupled Electron Transfer Reaction with Quasi Diabatic Propagation Scheme”, J. Phys. Chem. A, 2019, 123, 2470. (Invited Paper for Young Scientists Special Issue)
2018
(32) Hunter, K.; Shakib, F.A.; Paesani, F. “Disentangling Coupling Effects in the Infrared Spectra of Liquid Water”, J. Phys. Chem. B, 2018, 122, 10754.
(31) Mandal, A.; Shakib, F.A.; Huo, P. “Investigating Photoinduced Proton Coupled Electron Transfer Reaction using Quasi Diabatic Dynamics Propagation”, J. Chem. Phys. 2018, 148, 244102.
2017
(30) Shakib, F.A.; Huo, P. “Ring Polymer Surface Hopping: Incorporating Nuclear Quantum Effects into Nonadiabatic Molecular Dynamics Simulations”, J. Phys. Chem. Lett. 2017, 8, 3073–3080.
2016
(29) Shakib, F.A.; Hanna, G. “Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants”, J. Chem. Theory Comput., 2016, 12, 3020–3029.
(28) Shakib, F.A.; Hanna, G. “New Insight into the Nonadiabatic State Population Dynamics of Model Proton-Coupled Electron Transfer Reactions from the Mixed Quantum-Classical Liouville Approach”, J. Chem. Phys.2016, 144, 024110.
(27) Bundhun, A; Momeni, M.R.; Shakib, F.A.; Ramasami, P.; Gaspar, P.P.; Shaefer, H.F. “Toward Unsaturated Stannylenes Y2Z=Sn: and Related Compounds with Triplet Electronic Ground States”, RSC Adv., 2016, 6, 53749–53759.
2014
(26) Shakib, F.A.; Hanna, G. “An Analysis of Model Proton-Electrin Transfer Reactions via the Mixed Quantum-Classical Liouville Approach”, J. Chem. Phys. 2014, 141, 044122.
2013
(25) Naderi, F.; Momeni, M. R.; Shakib, F.A. “Theoretical Study of Highly Doped Heterofullerene Derivatives from the D6h Symmetry C36 Cage”, J. Theor. Comput. Chem. 2013, 12, 1350067.
(24) Sojudi, A.; Shakib, F.A.; Momeni, M.R.; Imani, M.; Shojaee, S. “Estimating the Stability and Reactivity of Acyclic and Cyclic Mono-heteroatom Substituted Germylenes: A Density Functional Theory Investigation”, Comput. Theor. Chem. 2013, 1009, 81-85.
2012
(23) Naderi, F.; Momeni, M. R.; Shakib, F. A. “Theoretical Study of Highly Doped Heterofullerenes Evolved from the Smallest Fullerene Cage”, Struct. Chem. 2012, 23, 1503-1508.
(22) Poursalemi, F.; Azarsa, A.; Momeni, M.R.; Shakib, F.A. “A DFT Study on the Structural and Electronic Properties of Td and C2 Symmetry C24X4 and C22X6 Heterofullerenes (X = B, Al, N, and P)”, Comput. Theor. Chem. 2012, 994, 14-18.
(21) Naderi, F.; Momeni, M.R.; Shakib, F.A. “A Density Functional Theory Study on the Stability and Ligand Properties of the Different Substituted Phenyl Carbenes”, Int. J. Phys. Sci. 2012, 7, 2439-2444.
(20) Momeni, M.R.; Shakib, F.A. “Beyond Conventional N-heterocyclic Silylenes: A Density Functional Approach toward Structural Features and Catalytic Applications”, Comput. Theor. Chem., 2012, 985, 62-66.
2011
(19) Shakib, F.A.; Momeni, M.R.; Wu, J.I.; Schleyer, P.v.R.; Azizi, Z.; Ghambarian M. “[n]Imperilenes: Stacked [n]Trannulenes Separated by Planar Cycloalkane Rings”, Org. Lett, 2011, 13, 3600-3603.
(18) Shakib, F.A.; Momeni, M. R. “Isolation: A Strategy for Obtaining Highly Doped Heterofullerenes”, Chem. Phys. Lett, 2011, 514, 321-324.
(17) Momeni, M.R.; Shakib, F.A.; Azizi, Z. “New Generation of Dialkylsilylenes with Stabilities Comparable to Diaminosilylenes: A Theoretical Study”, J. Phys. Chem. A, 2011, 115, 10550-10555.
(16) Momeni, M.R.; Shakib, F.A. “Theoretical Description of Triplet Silylenes Evolved from H2Si=Si”,Organometallics, 2011, 30, 5027-5032.
(15) Shakib, F.A.; Momeni M.R. “Density Functional Investigation of Metal Encapsulated X@C12Si8Heterofullerene (X = Li+, Na+, K+, Be2+, Mg2+, Ca2+, Al3+, Ga3+)”, Physica B: Condensed Matter, 2011, 406, 1471-1476.
(14) Momeni, M. R.; Shakib, F.A. “Monoheteroatom Substituted Six-membered Carbenes: A Computational Survey of Stability and Reactivity”, Comput. Theor. Chem., 2011, 965, 101-106.
(13) Kassaee, M.Z.; Momeni, M.R.; Najafi, Z.; Shakib, F.A.; Zandi, H. “Effects of α-Cyclopropyl on Heterocyclic Carbenes Stability at DFT”, J. Phys. Org. Chem., 2011, 24, 1022-1029.
(12) Kassaee, M.Z.; Najafi, Z.; Shakib, F.A.; Momeni, M.R. “Stable Silylenes with Acyclic, Cyclic, and Unsaturated Cyclic Structures: Effects of Heteroatoms and Cyclopropyl α-Substituents at DFT”, J. Organomet. Chem., 2011, 696, 2059-2064.
(11) Kassaee, M.Z.; Ghambarian, M.; Shakib, F.A.; Momeni, M.R. “From Acyclic Dialkylcarbene to the Unsaturated Cyclic Heteroatom Substituted Ones: A Survey of Stability”, J. Phys. Org. Chem., 2011, 24, 351-359.
2010
(10) Kassaee, M.Z.; Shakib, F.A.; Momeni, M.R.; Ghambarian, M.; Musavi, S.M. “Carbenes with Reduced Heteroatom Stabilization: A Computational Approach”, J. Org. Chem., 2010, 75, 2539-2545.
(9) Momeni, M.R.; Shakib, F.A. “Stable C20-nSin Heterofullerenes (n ≤ 8): A DFT Approach”, Chem. Phys. Lett., 2010, 492, 137-141.
(8) Kassaee, M.Z.; Momeni, M.R.; Shakib, F.A.; Ghambarian, M. “Pyridine Derived N-heterocyclic Germylenes: A Density Functional Perspective”, J. Organomet. Chem., 2010, 695, 760-765.
(7) Kassaee, M.Z.; Momeni, M.R.; Shakib, F.A.; Ghambarian, M.; Musavi, S.M. “Novel α-Spirocyclic (Alkyl)(Amino)Carbenes at the Theoretical Crossroad of Flexibility and Rigidity”, Struct. Chem., 2010, 21, 593-598.
2009
(6) Kassaee, M.Z.; Shakib, F.A.; Momeni, M.R.; Ghambarian, M.; Musavi, S.M. “A DFT Study on Pyridine-derived N-heterocyclic Carbenes”, Tetrahedron, 2009, 65, 10093-10098.
(5) Kassaee, M.Z.; Ghambarian, M.; Musavi, S.M.; Shakib, F.A.; Momeni, M.R. “A Theoretical Investigation into Dimethylcarbene and its Diamino and Diphosphino Analogs: Effects of Cyclization and Unsaturation on the Stability and Multiplicity”, J. Phys. Org. Chem., 2009, 22, 919-924.
(4) Kassaee, M.Z.; Shakib, F.A.; Momeni, M.R.; Ghambarian, M.; Musavi, S.M. “Silabenzene through Divalent Precursors at Theoretical Levels”, Monatsh. Chem., 2009, 140, 33-38.
(3) Kassaee, M.Z.; Zandi, H.; Momeni, M.R.; Shakib, F.A.; Ghambarian, M. “Toward Stable N-heterocyclic silylenes at Theoretical Levels”, J. Mol. Struc-Theochem, 2009, 913, 16-21.
(2) Kassaee, M.Z.; Momeni, M.R.; Shakib, F.A.; Ghambarian, M.; Musavi, S.M. “Effects of Fused Benzene Rings on Tautomerizations and Inversions of Benzo, Azabenzo, and Oxabenzocycloheptatrienes at Theoretical Levels”, Struct. Chem., 2009, 20, 517-524.
2008
(1) Kassaee, M.Z.; Musavi, S.M.; Momeni, M.R.; Shakib, F.A.; Ghambarian, M. “How Steric Effects Favor Thiepins over their Benzene Sulfide Tautomers at Theoretical Levels?”, J. Mol. Struc-Theochem, 2008, 861, 117-121.