scholarly journals Bonding, Structure, and Stability of Clusters: Some Surprising Results from an Experimental and Theoretical Investigation in Gas Phase

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Melissa S. Caetano ◽  
Teodorico C. Ramalho ◽  
Tales G. Vieira ◽  
Arlan da Silva Gonçalves ◽  
Daiana T. Mancini ◽  
...  
Keyword(s):  
Dipole Moment ◽  
Gas Phase ◽  
Charge Distribution ◽  
Theoretical Investigation ◽  
Ground State ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Structure And Stability ◽  
Bonding Structure ◽  
Small Dipole

Structure and stability of clusters in the ground state were analyzed at the theoretical and experimental levels. Our experimental and theoretical findings showed that the clusters in gas phase tend to form mainly planar rings of four members. The symmetry and the small dipole moment in these specific configurations suggested that their stability could be associated with an alignment of the water molecules, maximizing attractive electrostatic interactions caused by changes in the charge distribution of the clusters.

scholarly journals On the Microwave Spectrum of Methane in the Atmospheres of the Outer Planets

1974 ◽  
Vol 65 ◽  
pp. 359-365
Author(s):  
Kenneth Fox
Keyword(s):  
Dipole Moment ◽  
Spectral Range ◽  
Ground State ◽  
Microwave Spectrum ◽  
Outer Planets ◽  
Small Dipole ◽  
Line Strengths

The existence of a small dipole moment in the vibronic ground state of methane leads to transitions in the microwave spectral range. Frequencies and line strengths appropriate to the atmospheres of the outer planets are presented.

Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

2020 ◽  
pp. 1-20
Author(s):  
Yingying Zhang ◽  
Kamran Haider ◽  
Divya Kaur ◽  
Van A. Ngo ◽  
Xiuhong Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dipole Moment ◽  
Electrostatic Interactions ◽  
Hybrid Methods ◽  
Force Fields ◽  
Proton Channel ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Continuum Electrostatics ◽  
Hydrogen Bond Networks

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

Characterizing the water wire in the Gramicidin channel found by Monte Carlo sampling using continuum electrostatics and in molecular dynamics trajectories with conventional or polarizable force fields

2020 ◽  
pp. 2042001
Author(s):  
Yingying Zhang ◽  
Kamran Haider ◽  
Divya Kaur ◽  
Van A. Ngo ◽  
Xiuhong Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dipole Moment ◽  
Electrostatic Interactions ◽  
Hybrid Methods ◽  
Force Fields ◽  
Proton Channel ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Continuum Electrostatics ◽  
Hydrogen Bond Networks

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

Microwave Spectrum of 1-Butene Oxide

1978 ◽  
Vol 33 (11) ◽  
pp. 1312-1322
Author(s):  
S. O. Ljunggren ◽  
P. J. Mjöberg ◽  
J . E. Bäckvall
Keyword(s):  
Dipole Moment ◽  
Gas Phase ◽  
Internal Rotation ◽  
Barrier Height ◽  
Excited States ◽  
Ground State ◽  
Microwave Spectrum ◽  
Frequency Region ◽  
Centrifugal Distortion ◽  
Vibrationally Excited

The microwave spectrum of 1-butene oxide in the gas phase has been studied in the frequency region 18.0-39.0 GHz. The spectrum observed arose from a rotamer with a dihedral H-C2-C3-C4 angle of 59° ± 1°. In addition to several Q-branch progressions the spectrum contained several long perpendicular RP and PR progressions. However, of the ground state lines, only the intermediate PR transitions showed internal rotation splittings that could be resolved to yield a barrier height of 3.02 kcal mol-1. The value derived from the line splittings of the first excited methyl torsional state was slightly higher (3.17 kcal mol-1) but must be regarded as being less reliable. The components of the dipole moment, the rotational constants, and the quartic and sextic centrifugal distortion coefficients for the ground state and three vibrationally excited states were determined.

scholarly journals Correlations in hydrochloride drugs with diverse pharmacological activities. Role of N-H…Cl bonds

2020 ◽  
Vol 10 (3) ◽  
pp. 5536-5547
Keyword(s):  
Dipole Moment ◽  
Gas Phase ◽  
Dipole Moments ◽  
Antihypertensive Agents ◽  
Water Molecules ◽  
Electrophilicity Index ◽  
Pharmacological Activities ◽  
Molecular Weights ◽  
Solvation Energies

In this work, the structural and vibrational properties of sixteen hydrochloride/hydrobromide drugs with different pharmacological activities have been compared and analysed in order to find some correlations among their properties and, mainly elucidate the role of N-H•••Cl bonds in them. Here, the properties of ten alkaloids: tropane, gramine, morphine, cocaine, methadone, naloxone, heroin and scopolamine as hydrochloride and hydrobromide including, the psychotropic 2-CB agent; three antihistaminic: diphenhydramine, cyclizine and promethazine and; three antihypertensive tolazoline, clonidine and guanfacine agents have been evaluated. All properties were predicted in gas phase and aqueous solution by using the hybrid B3LYP/6-31G* method and the same were evaluated in functions of their molecular weights. Here, stabilization and solvation energies, dipole moments and volumes in both media, atomic MK charges and bond N-H and N+Cl- lengths, N-H stretching modes of N-HCl bonds of hydrochloride and their cationic species and, frontier orbitals together with global electrophilicity and nucleophilicity descriptors were compared for those sixteen drugs. The results have shown that bonds N+Cl- lengths of all hydrochloride species are higher in solution, as compared with the values in gas phase. Hydrochloride species of alkaloids and antihistaminic agents in both media present higher positive MK values on the N atoms of N-HCl bonds while the species related to antihypertensive agents show higher negative MK values on the N atoms or low positive values. The species of guanfacine presents the higher number of donors and acceptors groups, higher dipole moment value in solution, low bond N-H lengths, higher negative charge on the N atom of N-HCl bond and, higher global electrophilicity index. Hydrochloride species of scopolamine and heroin present the more negative solvation energies while tolazoline the lower value. Hydrochloride species of 2-CB and diphendramine show the higher expansions volumes in solution while the species of naloxone, scopolamine and cocaine evidence volumes contractions in this medium. These studies show that the knowledge of hydration degrees, that is, the number of water molecules that hydrate the hydrochloride species are essential to understand the hydration process of these species in relation to the differences observed in solvation energies, volume variations and dipole moment values.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

scholarly journals The Microwave Spectrum of 3,4-Dihydro-1,2-Pyran

1985 ◽  
Vol 40 (9) ◽  
pp. 913-919
Author(s):  
Juan Carlos López ◽  
José L. Alonso
Keyword(s):  
Dipole Moment ◽  
Excited States ◽  
Ground State ◽  
Principal Axis ◽  
Microwave Spectrum ◽  
Average Intensity ◽  
Ring Conformation ◽  
Vibrationally Excited ◽  
Rotational Constants ◽  
Displacement Measurements

Abstract The rotational transitions of 3,4-dihydro-1,2-pyran in the ground state and six vibrationally excited states have been assigned. The rotational constants for the ground state (A = 5198.1847(24), B = 4747.8716(24) and C = 2710.9161(24) have been derived by fitting μa, μb and μc-type transitions. The dipole moment was determined from Stark displacement measurements to be 1.400(8) D with its principal axis components |μa| =1.240(2), |μb| = 0.588(10) and |μc| = 0.278(8) D. A model calculation to reproduce the ground state rotational constants indicates that the data are consistent with a twisted ring conformation. The average intensity ratio gives vibrational separations between the ground and excited states of the ring-bending and ring-twisting modes of ~ 178 and ~ 277 cm-1 respectively.

scholarly journals Negative ion photoelectron spectroscopy confirms the prediction that D3h carbon trioxide (CO3) has a singlet ground state

2016 ◽  
Vol 7 (2) ◽  
pp. 1142-1150 ◽  
Author(s):  
David A. Hrovat ◽  
Gao-Lei Hou ◽  
Bo Chen ◽  
Xue-Bin Wang ◽  
Weston Thatcher Borden
Keyword(s):  
Gas Phase ◽  
Ground State ◽  
Photoelectron Spectroscopy ◽  
Radical Anion ◽  
Negative Ion ◽  
Singlet Ground State

The CO3 radical anion (CO3˙−) has been formed by electrospraying carbonate dianion (CO32−) into the gas phase.

scholarly journals Preparation and the Microwave and Infrared Spectra of Vinyl Ketene

1979 ◽  
Vol 34 (11) ◽  
pp. 1269-1274 ◽  
Author(s):  
Erik Bjarnov
Keyword(s):  
Dipole Moment ◽  
Gas Phase ◽  
Infrared Spectra ◽  
Room Temperature ◽  
Normal Modes ◽  
Spectroscopic Constants ◽  
Electrical Dipole ◽  
Electrical Dipole Moment ◽  
Vacuum Pyrolysis ◽  
Modes Of Vibration

Vinyl ketene (1,3-butadiene-1-one) has been synthesized by vacuum pyrolysis of 3-butenoic 2-butenoic anhydride. The microwave and infrared spectra of vinyl ketene in the gas phase at room temperature have been studied. The trans-rotamer has been identified, and the spectroscopic constants were found to be Ã= 39571(48) MHz, B̃ = 2392.9252(28) MHz, C̃ = 2256.0089(28) MHz, ⊿j = 0.414(31) kHz, and ⊿JK = - 34.694(92) kHz. The electrical dipole moment was found to be 0.987(23) D with μa = 0.865(14) D and μb = 0.475(41) D. A tentative assignment has been made for 17 of the 21 normal modes of vibration

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