On the chemical consequences of long-range interactions in chiral systems

1975 ◽  
Vol 28 (6) ◽  
pp. 1161 ◽  
Author(s):  
PE Schipper
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
Intermolecular Forces ◽  
Statistical Thermodynamic ◽  
Thermodynamic Quantities ◽  
Redox Potentials ◽  
Chiral Molecules ◽  
Long Range Interactions ◽  
Three Stages ◽  
Chiral Systems

The chemical manifestations of discrimination in long-range (non- contact) interactions of chiral molecules are analysed in three stages. A simple thermodynamic model is used to establish a method of presenting experimental data (such as differences in racemization rates, solubilities and redox potentials of pure enantiomers in non- associating chiral media) in terms of well defined thermodynamic discriminations. The thermodynamic quantities are then related directly to discriminations in intermolecular interactions through a statistical thermodynamic treatment. Estimates of the discrimination in intermolecular forces from experimental thermodynamic data suggest that only electrostatic interactions are sufficiently large to account for the experimentally observed values of the discrimination.

scholarly journals Polarizable embedding for simulating redox potentials of biomolecules

2019 ◽  
Vol 21 (22) ◽  
pp. 11642-11650 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Description ◽  
Biological Macromolecules ◽  
Classical Approach ◽  
Redox Potentials ◽  
Computational Protocol ◽  
Polarizable Embedding

We present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters.

scholarly journals Designing BH3-mimetic Peptide Inhibitors for the Viral Bcl-2 Homologs A179L and BHRF1: Importance of long-range electrostatic interactions

2021 ◽  
Author(s):  
C. Narendra Reddy ◽  
Ramasubbu Sankararamakrishnan
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
African Swine Fever Virus ◽  
Sequence Similarity ◽  
African Swine Fever ◽  
Barr Virus ◽  
Long Range Interactions ◽  
Infected Cells ◽  
Epstein Barr ◽  
Bh3 Mimetic

Viruses have evolved strategies to prevent apoptosis of infected cells at early stages of infection. The viral proteins (vBcl-2s) from specific viral genes adopt a helical fold that is structurally similar to that of mammalian anti-apoptotic Bcl-2 proteins and exhibit little sequence similarity. Hence vBcl-2 homologs are attractive targets to prevent viral infection. However, very few studies have focused on developing inhibitors for vBcl-2 homologs. In this study, we have considered two vBcl-2 homologs, A179L from African swine fever virus and BHRF1 from Epstein-Barr virus. We generated two sets of 8000 randomized BH3-like sequences from eight wild-type pro-apoptotic BH3 peptides. During this process, the four conserved hydrophobic residues and an Asp residue were retained at their respective positions and all other positions were substituted randomly without any bias. We constructed 8000 structures each for A179L and BHRF1 in complex with BH3-like sequences. Histograms of interaction energies calculated between the peptide and the protein resulted in negatively skewed distributions. The BH3-like peptides with high helical propensities selected from the negative tail of respective interaction energy distributions exhibited more favorable interactions with A179L and BHRF1 and they are rich in basic residues. Molecular dynamics studies and electrostatic potential maps further revealed that both acidic and basic residues favorably interact with A179L while only basic residues have the most favorable interactions with BHRF1. As in mammalian homologs, the role of long range interactions and non-hotspot residues have to be taken into account while designing specific BH3-mimetic inhibitors for vBcl-2 homologs.

INTERMOLECULAR POTENTIALS IN LIQUID CRYSTALS: COMPARISON BETWEEN SIMULATIONS AND NMR EXPERIMENTS

1999 ◽  
Vol 10 (02n03) ◽  
pp. 403-413 ◽  
Author(s):  
RAYMOND T. SYVITSKI ◽  
JAMES M. POLSON ◽  
E. ELLIOTT BURNELL
Keyword(s):  
Liquid Crystals ◽  
Long Range ◽  
Short Range ◽  
Intermolecular Forces ◽  
Order Parameters ◽  
Intermolecular Potential ◽  
Nmr Data ◽  
Long Range Interactions ◽  
Orientational Ordering ◽  
Best Fit

The anisotropic intermolecular forces responsible for the orientational ordering in liquid crystals are probed by comparing Monte Carlo (MC) simulations with experimental nuclear magnetic resonance (NMR) results for solutes in nematic liquid crystals. In a special liquid crystal mixture where all long-range interactions are assumed to be minimized, the models for short-range interactions which best fit NMR experimental solute order parameters also best fit solute order parameters from MC simulations of hard ellipsoids. This is taken as an indication that in this special mixture the intermolecular potential is dominated by short-range forces. However, for liquid crystals where long-range interactions are important, simulations of hard ellipsoids with point quadrupoles cannot reproduce even the gross effects observed with experimental NMR data.

Simulating Redox Potentials of Biomolecules: the Case of Cryptochrome 1 from Arabidopsis thaliana

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Redox Potential ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Estimate ◽  
Theoretical Description ◽  
Redox Potentials ◽  
Redox Active ◽  
Solvent Polarization ◽  
Cryptochrome 1

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present the results of computational studies of the redox potential of flavin adenine dinucleotide (FAD) in cryptochrome 1 from <i>Arabidopsis thaliana</i> (Cry1At). The special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The theoretical estimate (0.07 V) of the midpoint reduction potential of FAD in Cry1At is reported for the first time and is in good agreement with available experimental data.

Intermolecular forces

1975 ◽  
Vol 272 (915) ◽  
pp. 5-12 ◽  
Keyword(s):  
Long Range ◽  
Molecular Interactions ◽  
Short Range ◽  
Intermolecular Forces ◽  
Electron Exchange ◽  
Inverse Power ◽  
Charge Distributions ◽  
Electrostatic Component ◽  
Electrostatic Induction ◽  
Long Range Interactions

The nature of molecular interactions is examined. Intermolecular forces are divided into long-range and short-range components; the former operate at distances where the effects of electron exchange are negligible and decrease as an inverse power of the separation. The long-range interactions may be subdivided into electrostatic, induction and dispersion contributions, where the electrostatic component is the interaction of the permanent charge distributions and the others originate in the fluctuations in the distributions. Typical magnitudes of the various contributions are given. The forces between macroscopic bodies are briefly considered, as are the effects of a medium. Some of the manifestations of molecular interactions are discussed.

Simulating Redox Potentials of Biomolecules: the Case of Cryptochrome 1 from Arabidopsis thaliana

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Redox Potential ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Estimate ◽  
Theoretical Description ◽  
Redox Potentials ◽  
Redox Active ◽  
Solvent Polarization ◽  
Cryptochrome 1

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present the results of computational studies of the redox potential of flavin adenine dinucleotide (FAD) in cryptochrome 1 from <i>Arabidopsis thaliana</i> (Cry1At). The special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The theoretical estimate (0.07 V) of the midpoint reduction potential of FAD in Cry1At is reported for the first time and is in good agreement with available experimental data.

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