Anela Ivanova

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Papers by Anela Ivanova

Lysosome-targeting pH indicator based on peri-fused naphthalene monoimide with superior stability for long term live cell imaging

Journal of Materials Chemistry B

Lysosomal pH is altered in many pathophysiological conditions. We describe synthesis and spectral... more

Revealing the Origin of the Specificity of Calcium and Sodium Cations Binding to Adsorption Monolayers of Two Anionic Surfactants

The Journal of Physical Chemistry B

Transient absorption, femtosecond dynamics, vibrational coherence and molecular modelling of the photoisomerization of N-salicylidene-o-aminophenol in solution

Physical Chemistry Chemical Physics

This article presents a study of the excited state relaxation dynamics of N-salycylidene-o-aminop... more

Identification and computational characterization of isomers with cis and trans amide bonds in folate and its analogues

Physical Chemistry Chemical Physics

MD simulations and first-principles electronic structure calculations reveal viable configuration... more

Testing the limits of model membrane simulations-bilayer composition and pressure scaling

Journal of computational chemistry, Jan 30, 2018

Studying transfer of bioactive compounds across cell membranes by simulations attracts growing at... more Studying transfer of bioactive compounds across cell membranes by simulations attracts growing attention. To perform such calculations accurately, it is necessary to verify the validity of computational protocols established for description of unperturbed lipid bilayers also with translocating substances present. The current work reports the results from 1 μs long atomistic molecular dynamics simulations of two types of model plasma membranes-one built of a single phospholipid (DPPC) and one constructed of four types of phospholipids-in the presence of a drug-peptide complex experimentally known to cross cell membranes. The influence of membrane composition and of applied pressure scaling algorithm on the simulations outcome is analyzed with particular focus on membrane structure and on complex-lipid interactions during the initial penetration stage. It is found that the mixed composition of the membrane is important for correct assessment of the interactions with the complex both f...

Characterization of the interaction forces in a drug carrier complex of doxorubicin with a drug-binding peptide

Chemical biology & drug design, 2018

Polypeptide-based materials are used as building blocks for drug delivery systems aimed at toxici... more Polypeptide-based materials are used as building blocks for drug delivery systems aimed at toxicity decrease in chemotherapeutics. A molecular-level approach is adopted for investigating the non-covalent interactions between doxorubicin and a recently synthesized drug-binging peptide as a key part of a system for delivery to neoplastic cells. Molecular dynamics simulations in aqueous solution at room and body temperature are applied to investigate the structure and the binding modes within the drug-peptide complex. The tryptophans are outlined as the main chemotherapeutic adsorption sites, and the importance of their placement in the peptide sequence is highlighted. The drug-peptide binging energy is evaluated by density functional theory calculations. Principal component analysis reveals comparable importance of several types of interaction for the binding strength. π-Stacking is dominant, but other factors are also significant: intercalation, peptide backbone stacking, electrostat...

Density Functional Theory Assessment of the Environment Polarity Effect on Polyaniline-Water Coupling

The journal of physical chemistry. A, Jan 9, 2017

Crystallization water plays an important role in the self-organization of oligomer chains in cond... more Crystallization water plays an important role in the self-organization of oligomer chains in conducting polyaniline. In order to quantify the interaction between emeraldine salt and such a water, models containing a tetramer in bipolaronic or polaronic form, chloride counterions, and an explicit water molecule are used. Different initial positions of water with respect to the oligomer chain-tangential and vertical-are considered. Various media are simulated by introducing an implicit solvent continuum of decreasing polarity. The DFT-D3/PCM computational approach is employed to examine the behavior of the systems in several aspects-the role of the explicit water position and the effect of the environment polarity on the spatial structure, energetics, charge distribution, and the frontier molecular orbital energies. The strength of hydrogen bonding and the patterns of charge redistribution invoked by the water molecule are discussed. The study establishes trend lines in the variation ...

format_quotePolyaniline structures are most stable in water; dipole moments vary significantly across solvents, affecting interaction energy by 3-16 kcal/mol.format_quote

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Fully Doped Oligomers of Emeraldine Salt: Polaronic versus Bipolaronic Configuration

The Journal of Physical Chemistry B, 2011

Calculations for model oligomers of the emeraldine salt with UBLYP/6-31G*/PCM are performed. The ... more Calculations for model oligomers of the emeraldine salt with UBLYP/6-31G*/PCM are performed. The models differ in number of monomers, in the position of the counterions (Cl(-)), and in multiplicity. The molecular features affected most prominently by the protonation, namely, structure, energetics, and electron and spin density partitioning are analyzed. The results show unequivocally that the studied molecular characteristics are essentially size independent. The octamer profiles of all parameters are repeated in the dodecamer and the hexadecamer. The bipolaronic forms are energetically more favorable than the polaronic ones within the chosen protocol. The electronic structure in the intermediate multiplicities differs from the bipolaronic and polaronic periodicity. The geometrical changes and electron density redistribution upon increase of multiplicity illustrate the pathway of intramolecular bipolaron-polaron conversion. The orbital analysis rationalizes the observed behavior of the oligomers.

Understanding the Fluorescence of TADF Light-Emitting Dyes

The Journal of Physical Chemistry A, 2016

Figure S1. Absorption (top) and emission (bottom) transitions of DMATPhA-BPh-DPhBP; the coefficie... more

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Synthesis, magnetic properties and theoretical calculations of novel nitronyl nitroxide and imino nitroxide diradicals grafted on terpyridine moiety

by Martin Baumgarten, Anela Ivanova, and Ahmed Geies

Polyhedron, 2003

The synthetic route based on Stille coupling between tributyltinpyridyl derivatives and bromo sub... more The synthetic route based on Stille coupling between tributyltinpyridyl derivatives and bromo substituted mono-and dipyridylcarbaldehyde is used for the synthesis of 5,5ƒ-diformyl-2,2?:6?,2ƒ-terpyridine (8). A sequence of Ullman coupling with 2,3bis(hydroxylamino)-2,3-dimethylbutane followed by oxidation under phase transfer conditions affords either 5,5ƒ-Bis(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolidin-2-yl)2,2?:6?,2ƒ-terpyridine (10) (diNN-Terpy) or the related 5,5ƒ-Bis(1-oxyl-4,4,5,5-tetramethylimidazolidin-2-yl)2,2?:6?,2ƒ-terpyridine (11) (diIN-Terpy), where both biradicals display clear intramolecular ferromagnetic interaction between the single spin units as evidenced by ESR spectroscopy. Quantum chemical calculations (ROHF/AM1) are performed showing the triplet ground-state for both 10 and 11 radicals. #

format_quotePure organic ferromagnets demonstrate a critical role of intramolecular exchange interaction (J) in designing novel organic-based magnets.format_quote

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Molecular Dynamics Simulation of the Aggregation Patterns in Aqueous Solutions of Bile Salts at Physiological Conditions

The Journal of Physical Chemistry B, 2015

Classical molecular dynamics simulations are employed to monitor the aggregation behavior of six ... more Classical molecular dynamics simulations are employed to monitor the aggregation behavior of six bile salts (nonconjugated and glycine- and taurine-conjugated sodium cholate and sodium deoxycholate) with concentration of 10 mM in aqueous solution in the presence of 120 mM NaCl. There are 150 ns trajectories generated to characterize the systems. The largest stable aggregates are analyzed to determine their shape, size, and stabilizing forces. It is found that the aggregation is a hierarchical process and that its kinetics depends both on the number of hydroxyl groups in the steroid part of the molecules and on the type of conjugation. The micelles of all salts are similar in shape-deformed spheres or ellipsoids, which are stabilized by hydrophobic forces, acting between the steroid rings. The differences in the aggregation kinetics of the various conjugates are rationalized by the affinity for hydrogen bond formation for the glycine-modified salts or by the longer time needed to achieve optimum packing for the tauro derivatives. Evidence is provided for the hypothesis from the literature that the entirely hydrophobic core of all aggregates and the enhanced dynamics of the molecules therein should be among the prerequisites for their pronounced solubilization capacity for hydrophobic substances in vivo.

Systematic derivation and testing of AMBER force field parameters for fatty ethers from quantum mechanical calculations

by Maria Velinova and Anela Ivanova

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