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What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO & AIM analysis
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 9 , 2012 , Pages 787-796 ; 08943230 (ISSN) ; Abedin, A ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
Wiley
2012
Abstract
The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our...
In silico design of novel anticancer drugs with amino acid and carbohydrate building blocks to inhibit PIM kinases
, Article Molecular Simulation ; Volume 48, Issue 6 , 2022 , Pages 526-540 ; 08927022 (ISSN) ; Fattahi, A ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to...
New pathways of stability for NHCs derived from azole, di-azole, n-tetrazole, and ab-tetrazole, by DFT
, Article Journal of Molecular Modeling ; Volume 26, Issue 11 , 2020 ; Kassaee, M. Z ; Ayoubi Chianeh, M ; Fattahi, A ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2020
Abstract
We have investigated the pathways of stability for NHCs derived from azole, di-azole, n-tetrazole, and ab-tetrazole (1a, 2a, 3a, and 4a, respectively), at the M06/6-311++G** level of theory. Optimization and vibrational frequency calculations of ground states (GS) and transition states (TS) are performed to identify Gibbs free energies and nature of stationary points, respectively. Two possible pathways of stability for 1a-4a are compared and contrasted which entail dimerization through hydrogen bonding (HB) and covalent bonding (CB). The CB pathway comprises head to head (HH) and head to tail (HT) dimerizations. Plausible reaction profiles are illustrated for 1a-4a along with the mechanism...
Mechanisms and kinetics of Thiotepa and tepa hydrolysis: DFT study
, Article Journal of Molecular Modeling ; Volume 18, Issue 8 , 2012 , Pages 3563-3576 ; 16102940 (ISSN) ; Fattahi, A ; Sharif University of Technology
Springer
2012
Abstract
N,N′,N″-triethylenethiophosphoramide (Thiotepa) and its oxo analogue (Tepa) as the major metabolite are trifunctional alkylating agents with a broad spectrum of antitumor activity. In vivo and vitro studies show alkylation of DNA by Thiotepa and Tepa can follow two pathways, but it remains unclear which pathway represents the precise mechanism of action. In pathway 1, these agents are capable of forming cross-links with DNA molecules via two different mechanisms. In the first mechanism, the ring opening reaction is initiated by protonating the aziridine, which then becomes the primary target of nucleophilic attack by the N7-Guanine. The second one is a direct nucleophilic ring opening of...
Stereoelectronic effects: A simple yet powerful tool to manipulate anion affinity
, Article Organic and Biomolecular Chemistry ; Volume 13, Issue 7 , Dec , 2015 , Pages 2170-2176 ; 14770520 (ISSN) ; Fattahi, A ; Kass, S.R ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
Different strategies are employed in designing strong and selective anion receptors but stereoelectronic effects have been largely ignored. In this work, the stereo configuration of a non-interacting ether is found to have a large impact of more than two orders of magnitude on the binding of a rigid diol with tetrabutylammonium chloride in acetonitrile-d3. A favorable carbon-oxygen dipole and an intramolecular C-H⋯OH hydrogen bond in an equatorially substituted ether is found to be energetically more important than a stabilizing hydrogen bond in the corresponding axially oriented alcohol. IR spectroscopy is also used to probe the structures of the bound complexes and several binding motifs...
Theoretical aspects of the enhancement of metal binding affinity by intramolecular hydrogen bonding and modulating p: K a values
, Article New Journal of Chemistry ; Volume 41, Issue 24 , 2017 , Pages 15110-15119 ; 11440546 (ISSN) ; Fattahi, A ; Sharif University of Technology
Royal Society of Chemistry
2017
Abstract
Polyols were used as model ligands for Mg2+, Ca2+, and Zn2+ complexes to study the role of the hydrogen bond network on the metal binding affinity and modulation of successive pKa values using density functional theory. The results confirm that the acidity of polyols dramatically increases upon metal complexation in the order Zn2+ > Mg2+ > Ca2+. For example, the three H-site positions in the hydroxyl groups of the heptaol, bound to Zn2+, are 11.2, 29.9, and 30.9 pKa units (in methanol) more acidic than those of pure heptaol. This acidity enhancement leads to making polyols as good ligands toward complexation. For instance, the formation constants of the heptaol in the presence of Zn2+, Mg2+,...
Theoretical investigation of the effect of hydrogen bonding on the stereoselectivity of the Diels-Alder reaction
, Article New Journal of Chemistry ; Volume 45, Issue 36 , 2021 , Pages 16760-16772 ; 11440546 (ISSN) ; Mahmoodi, M. M ; Fattahi, A ; Sharif University of Technology
Royal Society of Chemistry
2021
Abstract
In this article, we report the computational examination of the impact of hydrogen bonding (HB) on the stereoselectivity of a series of Diels-Alder (DA) reactions. Four different types of diene/dienophile couples were studied including (a) cyclopenta-2,4-dien-1-ol and heteroatom-substituted cyclopentenes, (b) substituted cyclopentadienes andN-protonated 2,5-dihydro-1H-pyrrole, (c) furan andN-protonated 5-azabicyclo[2.1.1]hex-2-ene, and (d)N-protonated cyclopenta-2,4-dien-1-amine and α,β-unsaturated carbonyl compounds. These systems were designed such that the HB can only exist in theexoreaction pathway. The optimized structures of the transition states (TSs) and products, along with the...
Inducing high exo selectivity in Diels–Alder reaction by dimethylborane substituent: a DFT study
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
In this work, the role of Lewis acid–base (LAB) interaction on the stereoselectivity of the Diels–Alder (DA) reaction has been studied by DFT in gas and solution (dichloromethane) phases. The calculations were performed at the B3LYP/6-311G++ (d, p) level. Two different series of DA reactions were investigated: (1)—three mono-substituted cyclopentadienes + dimethyl(vinyl)borane; (2)—five α,β-unsaturated carbonyl compounds + cyclopenta-2,4-dien-1-yldimethylborane. The reacting diene and dienophile pairs were chosen to restrict LAB interaction to the exo reaction pathway. It was found that in some of the examined cases, the favorable LAB interaction is so strong that it can lead to a completely...
Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed...
Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of...
Molecular interaction of fibrinogen with zeolite nanoparticles
, Article Scientific Reports ; Volume 9, Issue 1 , 2019 ; 20452322 (ISSN) ; Hosseini, A ; Taghavi, F ; Jafari, S ; Lotfabadi, A ; Ejtehadi, M. R ; Shahbazi, S ; Fattahi, A ; Ghasemi, A ; Barzegari, E ; Evini, M ; Saboury, A. A ; Shahri, S. M. K ; Ghaemi, B ; Ng, E. P ; Awala, H ; Omrani, F ; Nabipour, I ; Raoufi, M ; Dinarvand, R ; shahpasand, K ; Mintova, S ; Hajipour, M. J ; Mahmoudi, M ; Sharif University of Technology
Nature Publishing Group
2019
Abstract
Fibrinogen is one of the key proteins that participate in the protein corona composition of many types of nanoparticles (NPs), and its conformational changes are crucial for activation of immune systems. Recently, we demonstrated that the fibrinogen highly contributed in the protein corona composition at the surface of zeolite nanoparticles. Therefore, understanding the interaction of fibrinogen with zeolite nanoparticles in more details could shed light of their safe applications in medicine. Thus, we probed the molecular interactions between fibrinogen and zeolite nanoparticles using both experimental and simulation approaches. The results indicated that fibrinogen has a strong and...
Does gold cluster promote or scavenge radicals? A controversy at DFT
, Article Journal of Physical Organic Chemistry ; 2017 ; 08943230 (ISSN) ; Kassaee, M. Z ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2017
Abstract
Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au3 cluster on RO• vs its impacts on RO-H bond dissociation enthalpy, at B3LYP/ LACVP+* level (RH, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). In the presence of Au3 cluster, bond dissociation enthalpy of O-H bond and the spin density at the RO• oxygen are reduced dramatically. These are clear evidences for both the Au3 facilitation of the RO-H bond breakage and its scavenging of RO• radical. Since O-Au anchoring...
The free radical scavenging activity of lespedezacoumestan toward ˙OH radical: a quantum chemical and computational kinetics study
, Article Journal of Physical Organic Chemistry ; Volume 31, Issue 2 , February , 2018 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2018
Abstract
The free radical activity of lespedezacoumestan was investigated toward hydroxyl (˙OH) radical in polar and nonpolar media using density functional theory. Four reaction mechanisms including radical adduct formation, hydrogen atom transfer, sequential single electron-proton transfer (SET-PT), and sequential proton loss electron transfer were considered. The rate constants and branching ratio for all possible sites of reaction were calculated and reported for the first time. According to the obtained results, lespedezacoumestan reacts faster with ˙OH radical in aqueous solution than in nonpolar media. Also, lespedezacoumestan is an excellent ˙OH radical scavenger regardless of the environment...
Ionic liquid based on 6-amino-6-deoxy hexopyranose cation and BF4 ¯, PF6 ¯, and ClO4 ¯ as anions: a DFT study on the structural and electronic properties
, Article Journal of Physical Organic Chemistry ; Volume 31, Issue 5 , 2018 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2018
Abstract
In this study, the structural and electronic properties of a carbohydrate-based (6-amino-6-deoxy hexopyranose [ADHP]) ionic liquid were explored. The interactions among 3 anions (BF4 ¯, PF6 ¯, and ClO4 ¯) and ADHP as cation were investigated at B3LYP/6-311++G(d,p) level. Based on the calculated interaction energy, it was found that PF6 ¯ anion has the highest interaction energy with ADHP. It was found that the hydrogen bonds play an important role in the interaction of ion pairs. The nature of hydrogen bonds in the optimized ion pars was analyzed by using natural bond orbital analysis and the quantum theory of atoms in molecules. The linear relationship between electron density at the bond...
Does gold cluster promote or scavenge radicals? A controversy at DFT
, Article Journal of Physical Organic Chemistry ; Volume 31, Issue 3 , 2018 ; 08943230 (ISSN) ; Kassaee, M. Z ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2018
Abstract
Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au3 cluster on RO• vs its impacts on RO–H bond dissociation enthalpy, at B3LYP/ LACVP+* level (R═H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). In the presence of Au3 cluster, bond dissociation enthalpy of O–H bond and the spin density at the RO• oxygen are reduced dramatically. These are clear evidences for both the Au3 facilitation of the RO–H bond breakage and its scavenging of RO• radical. Since O–Au...
Influence of remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinonederivatives: A DFT study
, Article Journal of Physical Organic Chemistry ; Volume 32, Issue 4 , 2019 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2019
Abstract
In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H 2 O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy-1,4-benzoquinone. Noncovalent interaction reduced density gradient (NCI-RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm...
Influence of H-bonds on acidity of deoxy-hexose sugars
, Article Journal of Physical Organic Chemistry ; Volume 33, Issue 10 , June , 2020 ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2020
Abstract
The unusual monosaccharaides such as deoxy-hexose sugars, including methyl-pentose and aldo-pentose, are promising and important sugars in life science. However, little research on H-bond interactions in these systems has been reported. The aldo-pentose has a proton instead of the CH2OH group on C5; conversely, methyl-pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H-bonds on acidity of CH3-pentose sugars (L-fucose and L-rhamnose) and aldo-pentose sugars (D-xylose, L-lyxose, D-ribose, and L-arabinose) using B3LYP/6-311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy-hexose were found to be from 343 to...
Acidity enhancement of α-carbon of beta diketones via hydroxyl substituents: A density functional theory study
, Article Journal of Physical Organic Chemistry ; 2020 ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2020
Abstract
Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd
Acidity enhancement of α-carbon of beta diketones via hydroxyl substituents: A density functional theory study
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 3 , 2021 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd
Gold at crossroads of radical generation and scavenging at density functional theory level: Nitrogen and oxygen free radicals versus their precursors in the face of nanogold
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 1 , 2021 ; 08943230 (ISSN) ; Kassaee, M. Z ; Ayoubi Chianeh, M ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),...