Abstract：
:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and (•)OH have also been investigated.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Armaković S,Armaković SJ,Abramović BFdoi
10.1007/s00894-016-3101-2subject
Has Abstractpub_date
2016-10-01 00:00:00pages
240issue
10eissn
1610-2940issn
0948-5023pii
10.1007/s00894-016-3101-2journal_volume
22pub_type
杂志文章abstract：:Present theoretical study involves the delta shape complexes of beryllium, magnesium, and calcium where the metal atom interacts perpendicularly with disubstituted acetylene. Most of the complexes are found to be fairly stable. The dependence of second-hyperpolarizability on the basis set with increasing polarization ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2804-0
更新日期：2015-10-01 00:00:00
abstract：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-4330-y
更新日期：2020-03-07 00:00:00
abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1694-7
更新日期：2013-07-01 00:00:00
abstract：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4258-2
更新日期：2019-11-28 00:00:00
abstract：:The feasibility of electron transport conduction through a guanine base of DNA was investigated and then compared with another component of DNA, i.e., cytosine. A mathematical approach based on the jellium model using non-equilibrium Green's function combined with semi empirical extended Huckel theory was applied usin...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3856-8
更新日期：2018-11-01 00:00:00
abstract：:A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of s...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3395-8
更新日期：2017-08-01 00:00:00
abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1153-x
更新日期：2012-04-01 00:00:00
abstract：:Recent ab initio investigations of some complexes formed between carbon dioxide and its analogues carbonyl sulfide, carbonyl selenide, carbon disulfide, and thiocarbonyl selenide and the common bases ammonia, water, phosphine, and hydrogen sulfide have revealed significant differences between the properties of those c...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2562-4
更新日期：2015-02-01 00:00:00
abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0876-4
更新日期：2011-07-01 00:00:00
abstract：:Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accu...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0535-9
更新日期：2010-02-01 00:00:00
abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3301-4
更新日期：2017-04-01 00:00:00
abstract：:Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbital...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2159-y
更新日期：2014-03-01 00:00:00
abstract：:The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)2]+[Ag(CN)2]- (2) and [Ag(Imt)2]+[Ag(CN)2]- (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3970-2
更新日期：2019-03-08 00:00:00
abstract：:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2301-x
更新日期：2014-06-01 00:00:00
abstract：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-004-0216-7
更新日期：2004-12-01 00:00:00
abstract：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2554-4
更新日期：2015-03-01 00:00:00
abstract：:Here, we report a structure-based virtual screening of the ZINC database (containing about five million compounds) by computational docking and the analysis of docking energy calculations followed by in vitro screening against H. pylori urease enzyme. One of the compounds selected showed urease inhibition in the low m...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1310-2
更新日期：2012-07-01 00:00:00
abstract：:Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm withi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3116-8
更新日期：2016-10-01 00:00:00
abstract：:Electronic properties of Fe(2-10) clusters and their ions are described by an all-electron ab initio density functional theory computational analysis using the Handy's OPTX exchange and the gradient-corrected correlation functional of Perdew, Burke and Ernzerhof with a triple-zeta valence basis set plus polarization f...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1395-2
更新日期：2012-09-01 00:00:00
abstract：:We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charg...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3932-8
更新日期：2019-01-31 00:00:00
abstract：:The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concen...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-002-0107-8
更新日期：2003-02-01 00:00:00
abstract：:Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phospha...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0403-z
更新日期：2009-02-01 00:00:00
abstract：:In this study, the complete orthonormal sets of phi(alpha)-momentum space orbitals (where alpha = 1, 0, -1, -2, ...) obtained from the psi(alpha)-ETO in coordinate representation (I.I. Guseinov, J. Mol. Model., 9 (2003) 135) are reduced to the complete orthonormal sets of hyperspherical harmonics (HSH) by means of a F...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-005-0093-8
更新日期：2006-09-01 00:00:00
abstract：:The interaction between tetramethylcucurbit[6]uril (host) and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride (guest) was studied by 1H NMR, X-ray crystallography, electronic absorption spectroscopy, fluorescence emission spectra and quantum chemistry calculations. This experimental-computational study that indicated the h...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0243-2
更新日期：2007-12-01 00:00:00
abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4104-6
更新日期：2019-07-02 00:00:00
abstract：:Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4220-3
更新日期：2019-10-26 00:00:00
abstract：:Ethanol and water are the solvents most commonly used to extract flavonoids from propolis. Do hydrogen-bonding interactions exist between flavonoids and ethanol/water? In this work, this question was addressed by using density functional theory (DFT) to provide information on the hydrogen-bonding interactions between ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2968-2
更新日期：2016-04-01 00:00:00
abstract：:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1528-7
更新日期：2013-01-01 00:00:00
abstract：:Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) fo...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2707-0
更新日期：2015-06-01 00:00:00
abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1571-4
更新日期：2013-07-01 00:00:00
