Molecular conformations of ortho-substituted benzophenones

1976 ◽  
Vol 54 (2) ◽  
pp. 226-230 ◽  
Author(s):  
Felice Zuccarello ◽  
Salvatore Millefiori ◽  
Salvatore Trovato
Keyword(s):  
Electrostatic Interactions ◽  
Minimum Energy ◽  
Molecular Conformations ◽  
Relative Stabilities ◽  
Contour Maps ◽  
Semiempirical Approach ◽  
Relevant Role ◽  
Geometrical Data ◽  
Highly Strained ◽  
Good Agreement

The minimum energy conformations of some mono- and di-substituted benzophenones were determined from contour maps of potential energy calculated by a semiempirical approach. The electrostatic interactions play a relevant role in the relative stabilities when different minima are possible. Comparison with the available experimental data reveals a good agreement with geometrical data, and a poorer agreement with energies in highly strained conformations.

scholarly journals Which Is the Motion State of a Droplet on an Inclined Hydrophilic Rough Surface in Gravity: Pinned or Sliding?

2021 ◽  
Vol 11 (9) ◽  
pp. 3734
Author(s):  
Jian Dong ◽  
Youhai Guo ◽  
Long Jiao ◽  
Chao Si ◽  
Yinbo Bian ◽  
...  
Keyword(s):  
Rough Surface ◽  
Contact Angle Hysteresis ◽  
Minimum Energy ◽  
Contact Angles ◽  
Microfluidic Chips ◽  
Motion State ◽  
Receding Contact ◽  
Novel Design ◽  
Minimum Energy Dissipation ◽  
Good Agreement

The motion state of a droplet on an inclined, hydrophilic rough surface in gravity, pinned or sliding, is governed by the balance between the driving and the pinned forces. It can be judged by the droplet’s shape on the inclined hydrophilic rough surface and the droplet’s contact angle hysteresis. In this paper, we used the minimum energy theory, the minimum energy dissipation theory, and the nonlinear numerical optimization algorithm to establish Models 1–3 to calculate out the advancing/receding contact angles (θa/θr), the initial front/rear contact angles (θ1−0/θ2−0) and the dynamic front/rear contact angles (θ1−*/θ2−*) for a droplet on a rough surface. Also, we predicted the motion state of the droplet on an inclined hydrophilic rough surface in gravity by comparing θ1−0(θ2−0) and θ1−*(θ2−*) with θa(θr). Experiments were done to verify the predictions. They showed that the predictions were in good agreement with the experimental results. These models are promising as novel design approaches of hydrophilic functional rough surfaces, which are frequently applied to manipulate droplets in microfluidic chips.

A thermodynamic model of hemoglobin suitable for physiological applications

1990 ◽  
Vol 258 (3) ◽  
pp. C563-C577 ◽  
Author(s):  
T. Yoshida ◽  
M. Dembo
Keyword(s):  
Binding Sites ◽  
Electrostatic Interactions ◽  
Mean Field ◽  
Quantitative Model ◽  
Confidence Limits ◽  
Efficient Computation ◽  
Ligand Binding Sites ◽  
The Mean ◽  
Field Formalism ◽  
Good Agreement

We propose a quantitative model of the thermodynamics of hemoglobin in contact with its five major ligands (O2, CO2, Cl-, 2,3-bisphosphoglycerate, and H+). Our model incorporates the two-state formalism of J. Monod, J. Wyman, and J.P. Changeux (J. Mol. Biol. 12: 88-118, 1965) for treatment of quanternary transitions and also the mean field formalism of K. Linderstrom-Lang (C. R. Trav. Lab. Carlsberg Ser. Chim. 15: 1-30, 1924) for treatment of electrostatic interactions. On the basis of this approach, we develop an algorithm for the efficient computation of observable quantities, such as the occupancy of various ligand binding sites, and an objective statistical procedure for determining both maximum likelihood values and confidence limits of all the intrinsic thermodynamic parameters of hemoglobin. Finally, we show that the predictions of our theory are in good agreement with independent experimental observations.

Accurate heats of atomization and accurate bond lengths.: II. Polyenes and polyphenyls

1968 ◽  
Vol 46 (12) ◽  
pp. 2041-2051 ◽  
Author(s):  
Donald H. Lo ◽  
M. A. Whitehead
Keyword(s):  
Steric Hindrance ◽  
Bond Order ◽  
Minimum Energy ◽  
Stabilization Energy ◽  
Direct Measure ◽  
Bond Lengths ◽  
Molecular Stability ◽  
Linear Polyenes ◽  
Substituted Polyenes ◽  
Good Agreement

Accurate heats of atomization and bond lengths are calculated for several polyenes and polyphenyls, using the s.c.f.–l.c.a.o.–m.o. method described in Part I (1). Localization of π and σ bonds is found in the linear polyenes and in the diphenyl-substituted polyenes. The estimated stabilization energy per CC bond (SECC) gives a direct measure of the π electron conjugation and σ bond compression. Conjugation stabilization and steric hindrance are analyzed in 1,3-butadiene and biphenyl; the predicted geometries are in good agreement with experimental results. The minimum energy for any planar structure is found to be associated with the s.c.f. calculated bond lengths. The validity of pi bond order as a measure of molecular stability in the polyphenyls is discussed.

Ab Initio Theoretical Studies of Relative Stabilities and IR Spectrum of 5-Methylcytosine Tautomers

2003 ◽  
Vol 2003 (4) ◽  
pp. 195-199 ◽  
Author(s):  
Lida Ghassemzadeh ◽  
Majid Monajjemi ◽  
Karim Zare
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Relative Energy ◽  
Theoretical Studies ◽  
Functional Theory ◽  
Relative Stabilities ◽  
B3lyp Method ◽  
Wide Range ◽  
Good Agreement

The structure and relative energies of the tautomers of 5-methylcytosine in the gasphase and in different solvents are predicted using MP2 and density functional theory methods. The order of stability for these tautomers is C3>C1>C2>C4>C5>C6 calculated by MP2 and C1>C3>C2>C4>C5>C6 calculated by the B3LYP method. Relative energy calculations are performed in wide range of solvent dielectrics and in all solvents the oxo-amino C1 is predicted as the most stable tautomer. The infrared spectra of two dominant tautomers are calculated in the gas phase using HF and density functional theory. Good agreement between calculated (DFT) and experimental harmonic vibrational frequencies is found.

Embedded atom calculations of the equilibrium shapes of 5–60 atom palladium nanocrystals

1993 ◽  
Vol 8 (3) ◽  
pp. 455-461 ◽  
Author(s):  
A. Sachdev ◽  
R.I. Masel
Keyword(s):  
Minimum Energy ◽  
Wide Distribution ◽  
Embedded Atom Method ◽  
Palladium Clusters ◽  
Embedded Atom ◽  
Equilibrium Shapes ◽  
The Stability ◽  
Highly Strained ◽  
Palladium Particles ◽  
Particle Shapes

The embedded atom method (EAM) has been used to compare the stability of a series of small palladium clusters with 5–60 atoms and a variety of shapes. It is found that the 13- and 55-atom icosahedra and cubo-octahedra are stable at 0 K. However, other sized icosahedra and cubo-octahedra are unstable at 0 K. Upon annealing, the icosahedra and cubo-octahedra reconstruct into nonpolyhedral structures which are highly strained. The strained structures are much more stable than the icosahedron or cubo-octahedron except when there are 13 or 55 atoms in the cluster. Further, there are many disordered shapes which are within 0.01 eV of the minimum energy structures at all cluster sizes including 13 and 55 atoms. We observe transitions between these low energy structures in Monte Carlo calculations. These results suggest that at equilibrium one should rarely observe polyhedral palladium particles. Instead, most of the particles should be disordered. Further, there should be a wide distribution of particle shapes in agreement with experiment.

scholarly journals Rationalizing generation of broad spectrum antibiotics with the addition of a primary amine

2021 ◽  
Author(s):  
Nandan Haloi ◽  
Archit Kumar Vasan ◽  
Emily Jane Geddes ◽  
Arjun Prasanna ◽  
Po-Chao Wen ◽  
...  
Keyword(s):  
Free Energy ◽  
Primary Amine ◽  
Electrostatic Interactions ◽  
Degrees Of Freedom ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Gram Negative ◽  
Molecular Conformations ◽  
Energy Calculations ◽  
Cell Accumulation

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and while forming favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.

scholarly journals A Theoretical Stereoselectivity Model of Photochemical Denitrogenations of Diazoalkanes Towards Strained 1,3-Dihalogenated Bicyclobutanes

2020 ◽  
Author(s):  
Jingbai Li ◽  
Rachel Stein ◽  
Steven Lopez
Keyword(s):  
Minimum Energy ◽  
Photochemical Reactions ◽  
Basis Set ◽  
Strained Molecules ◽  
Complete Active Space ◽  
Active Space ◽  
Self Consistent Field ◽  
Shoulder Region ◽  
Highly Strained ◽  
Diastereomeric Excess

<p>Photochemical reactions exemplify ‘green’ chemistry and are essential for synthesizing highly strained molecules with mild conditions with light. The light-promoted denitrogenation of bicyclic azoalkanes affords functionalized, stereoenriched bicyclo[1.1.0]butanes. We revisited these reactions with multireference calculations and non-adiabatic molecular dynamics (NAMD) simulations for a series of diazabicyclo[2.1.1]hexenes to predict the photophysics, reactivities, and stereoselectivities. We used complete active space self-consistent field (CASSCF) calculations with an (8,8) active space and ANO-S-VDZP basis set; the CASSCF energies were corrected with CASPT2(8,8)/ANO-S-VDZP. The excitation is consistently n→π* and ranges from 3.77–3.91 eV for the diazabicyclo[2.1.1]hexenes. Minimum energy path calculations showed stepwise C–N bond breaking and led to a minimum energy crossing point, which favors the stereochemical ‘double inversion’ bicyclobutane product. Wigner sampling of <b>1</b> provided Franck-Condon points for 692 NAMD trajectories. We identified competing complete stereoselective and stereochemical scrambling pathways. The stereoselective pathways feature concerted bicyclobutane inversion and N<sub>2</sub> extrusion. The stereochemical scrambling pathways involve N<sub>2</sub> extrusion followed by bicyclobutane planarization, leading to non-stereoselective outcomes. The predicted diastereomeric excess almost exactly match experiment (calc<i>.d.e.</i>=46% <i>vs.</i> exp<i>.d.e.</i>=47%). Our NAMD simulations with 672, 568, and 596 trajectories for <b>1-F</b>, <b>1-Cl</b>, and <b>1-Br</b> predicted diastereomeric excess (<i>d.e.</i>) of 94–97% for the double inversion products. Halogenation significantly perturbs the potential energy surface (PES) towards the retention products because of powerful hyperconjugative interactions. The n<sub>C</sub>→σ<sup>*</sup><sub>C–X</sub>,<sub> </sub>X = F, Cl, Br hyperconjugative interaction leads to a broadened shoulder region on the PES for double inversion.</p>

MINDO-Forces Study on the Relative Stabilities of Hydroxy- and Aminopyridine Tautomers

1985 ◽  
Vol 40 (12) ◽  
pp. 1278-1282 ◽  
Author(s):  
Salim M. Khalil
Keyword(s):  
Relative Stabilities ◽  
Experimental Values ◽  
Good Agreement

Relative stabilities of monosubstituted hydroxy- and aminopyridine tautomers have been calculated using the semiempirical MINDO-Forces MO method with full geometries optimization. The lactim tautomers proved to be more stable except in the case of 2-hydroxypyridine. The results are in good agreement with some theoretical and experimental values.

Relative stability of benziporphyrin and naphthiporphyrin tautomers and the emergence of macrocyclic diatropicity

2014 ◽  
Vol 12 (43) ◽  
pp. 8719-8736 ◽  
Author(s):  
Deyaa I. AbuSalim ◽  
Timothy D. Lash
Keyword(s):  
Relative Stability ◽  
Relative Stabilities ◽  
Good Agreement

The conformations and relative stabilities of a series of benziporphyrin and naphthiporphyrin tautomers were calculated and the diatropic properties of each of these species were assessed. The results were in good agreement with experimental observations and allow favorable delocalization pathways to be identified.

Ion Pair Formation and Solvation Energies in Solutions of Alkali Halides in Dimethyl Sulfoxide. II. Model Calculations

1975 ◽  
Vol 53 (7) ◽  
pp. 1007-1018 ◽  
Author(s):  
Merrill S. Goldenberg ◽  
Peeter Kruus ◽  
Stephen K. F. Luk
Keyword(s):  
Dimethyl Sulfoxide ◽  
Electrostatic Interactions ◽  
Minimum Energy ◽  
Alkali Halides ◽  
Dmso Molecule ◽  
Ion Pair ◽  
Model Calculations ◽  
Energy Calculations ◽  
Solvation Energies ◽  
Repulsive Forces

Energy calculations were carried out on models of molecular-level structures likely to be present in solutions of alkali halides in dimethyl sulfoxide (DMSO). Classical electrostatic interactions were assumed, and polarization of a DMSO molecule was assumed due to the fields of the ions only. The validity of this assumption was tested. DMSO molecules were represented by increasingly detailed models, with most calculations carried out with each molecule represented by 10 point charges and 9 polarizable bonds. A program including up to 14 such molecules and two ions was used for energy and distance calculations, and is made available. Polarization effects are as important as interactions between permanent charges for energy calculations. The configurations of minimum energy determined by classical electrostatics often do not involve overlap of the "hard-sphere radii" of neighboring species, so that the neglect of quantum mechanical repulsive forces seems justified. Energy cycles using the calculated energies for ion–solvent complexes predicted experimental cation enthalpies with some success. The form of the potential for vibration of a cation in a solvent shell was investigated and found in cases not to have an energy minimum at the shell center. Calculations including next-nearest solvating DMSO's indicate a rather loose structure. An energy profile for an anion moving from a solvent-separated ion pair position to a contact-ion pair position is presented.

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