Free jet rotational spectrum of the most stable conformer of 1-(2-fluorophenyl)-1-ethanol

The most stable conformer of chiral 1-(2-fluorophenyl)-1-ethanol is stabilized by a O–H?π interaction and it is at least 1 kcal/mol more stable than the remaining conformers. This is the result of a free jet millimeter–wave absorption spectroscopy investigation of the rotational spectra of the most abundant and O–d isotopic species.     

Vibrational spectroscopy of cis- and trans-formic acid in solid argon

Absorption spectra of cis and trans conformers of formic acid (HCOOH) isolated in solid argon are analyzed in the mid-infrared (4000-) and near-infrared (7800-) regions. The HCOOH absorption spectrum reveals matrix-site splitting for the trapped molecule. Narrowband tunable infrared radiation is used to pump a suitable vibrational transition of the trans conformer in order to promote site-selectively the conversion to the cis conformer and separate the spectral features of each site group. Several anharmonic resonances are identified for both conformers. The results of anharmonic vibrational ab initio calculations (CC-VSCF) for the trans and cis conformers of formic acid are reported and compared with the experimental spectra.     

Vibrational spectroscopy of trans and cis deuterated formic acid (HCOOD): Anharmonic calculations and experiments in argon and neon matrices

The absorption spectra of trans and cis conformers of deuterated formic acid (HCOOD) isolated in argon and neon matrices are analyzed in the mid-infrared and near-infrared spectral regions (7900-450 cm⁻¹). Vibrational excitation by narrow-band IR radiation is used to convert the lower-energy trans conformer to the higher-energy cis form. A large number of overtone and combination bands are identified. The results of anharmonic vibrational calculations (CC-VSCF) for both conformers are reported and compared to the experimental spectra.     

How universal are hydrogen bond correlations? A density functional study of intramolecular hydrogen bonding in low-energy conformers of α-amino acids

Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O–H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D–H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur.

Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials.     

FT‐Raman,FT‐IR spectra and DFT calculations on monomeric and dimeric structures of 5‐fluoro‐ and 5‐chloro‐salicylic acid

The experimental and theoretical study on the structures and vibrations of 5‐fluoro‐salicylic acid and 5‐chloro‐salicylic acid (5‐FSA and 5‐ClSA, C₇H₅FO₃ and C₇H₅ClO₃) is presented. The Fourier transform infrared spectra (4000–400 cm⁻¹) and the Fourier transform Raman spectra (4000–50 cm⁻¹) of the title molecules in the solid phase were recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman intensities and Raman scattering activities were calculated for a pair of molecules linked by the intermolecular O H···O hydrogen bond. The geometrical parameters and energies of 5‐FSA and 5ClSA were obtained for all eight conformers/isomers from density functional theory (DFT) (B3LYP) with 6‐311++G(d,p) basis set calculations. The computational results identified the most stable conformer of 5‐FSA and 5‐ClSA as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The spectroscopic and theoretical results were compared with the corresponding properties for 5‐FSA and 5‐ClSA monomers and dimer of C1 conformer. The optimized bond lengths, bond angles and calculated wavenumbers showed the best agreement with the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Vibrational and Conformational Analysis of 5-Methyl-2-Hexyne

Infrared and Raman spectra were obtained for 5- methyl-2-hexyne and wereinterpreted with the aid of normal coordinate calculations. The spectra and molecular mechanics calculations show the compound to exist in two spectroscopically distinguishable stable conformations, with the C₁ conformer being only a little more stable than the C_s, conformer. Vibrational assignments were made for both conformers.     

拉曼光谱法确定某些硅聚合物的构象稳定性(英文)

为了比较某些取代乙烯硅烷不同构象的相对稳定性 ,我们进行了一系列波数在 5 0 -35 0 0cm- 1间的拉曼光谱研究。本文所涉及的分子包括一 ,二卤 (F ,Cl,Br)代乙烯硅烷 ,甲基乙烯基二卤 (F ,Cl)代硅烷以及二甲基乙烯基—卤 (F ,Cl)代硅烷。对以上这些分子 ,我们进行了全电子相关Moller -Plesset微扰理论第二阶(MP2 )的从头 (abinitio)计算。我们仅引入两个比率因子 (scalingfactor)用以计算出液相中上述分子两种稳定构象的拉曼光谱。依据计算模拟所得的谱图 ,以及与实验所得的固相拉曼谱图的比较 ,我们便可判定哪种构象存在于固态之中。通过对液态样品拉曼谱峰的温度相关性研究以及对低温下样品的稀有气体溶液红外谱峰的温度相关性研究 ,我们测定了一系列乙烯硅烷分子两种稳定构象间的焓差 ,并将这些实验结果与上至 6-31 1 +G( 2d ,2 p)的一系列基组的微扰理论和密度泛函理论 (DFT)从头计算结果进行比较。     

An ab initio study of the harmonic and anharmonic force field and fundamental vibrational frequencies of performic acid

The harmonic and anharmonic force fields and fundamental vibrational frequencies of cis-cis and cis-trans performic acid are studied ab initio in the 4-31G basis set using geometries fully optimized at this level. The frequencies predicted for the cis-cis conformer are compared with those derived from spectroscopic observations on the most stable form. An extensive comparison is made between the changes in diagonal and off-diagonal quadratic and cubic force constants, and diagonal stretching quartic constants, in going from the chain to the ring structure in performic and formic acid, and features which these changes have in common are seen to support the view that there is a hydrogen bonding type of interaction in trans-formic acid despite its unfavorable geometry.     

Conformational Analysis of 1,2-Dichlorobutane

Vibrational spectra have been published and normal coordinate calculations have been made for 1,2-dichlorobutane.^1,2 Those calculations were limited to the three conformers that had all four carbon atoms coplanar. Molecular mechanics calculations have now shown a conformer that was omitted to be the second most abundant conformer. Therefore, normal coordinate calculations have been made for this conformer and molecular mechanics calculations have been made for all possible conformers.     

Toward ab initio potential energy surface for paclitaxel: a baccatin III conformational study

The ab initio conformational energy profile of baccatin III, the diterpene part of paclitaxel, a natural, taxoid anticancer agent, has been investigated using medium‐size basis sets including an electron correlation method (MP2/DFT). By exploiting the internal coordinates using random search methods, 39 conformers of baccatin III were found. The most stable conformer, competing with its 13‐C rotamers, was shown to have three intramolecular hydrogen bonds of 1, 7 and 13 hydroxyls to the carbonyl oxygen atoms of 2‐benzoate and 10‐ and 4‐acetate ester groups, respectively. The results of the polarizable continuum model (PCM) used to account for the dielectric effect of the environment show that in water, the delicate balances between intramolecular hydrogen bridges and general conformational preferences are conserved, at least in the absence of explicit solvent molecules. Copyright © 2016 John Wiley & Sons, Ltd.     

The structure of the gas-phase tyrosine–glycine dipeptide

The structural preferences of the neutral dipeptide Tyr–Gly have been investigated using a hierarchical selection scheme. This scheme consists of a hierarchy of increasingly more accurate electronic structure methods (single-point HF/3-21G* energy calculation, HF/3-21G* geometry optimization, B3LYP/6-31+G* geometry optimization, MP2/6-31+G* single-point energy calculation, and MP2/6-31+G* geometry optimization). The conformers are sorted according to their single-point or optimized energy, and only the most stable conformers according to one level are taken through to the next level of calculation. The defining structural characteristics in the 20 most stable Tyr–Gly conformers are the presence or absence of a folded arrangement of the peptide backbone (‘book’) and an OH···O hydrogen bond between the C-terminal hydroxyl group and the carbonyl oxygen of tyrosine (‘OHO’). The most stable conformer is of the book/OHO type. MP2 geometry optimization significantly alters the structure of the book-type conformers, increasing their degree of foldedness. Thus, care has to be taken when applying standard density functionals like B3LYP in structural studies of peptides with aromatic side chains.     

Raman spectroscopic characterization of a thiophene‐based active material for resistive organic nonvolatile memories

A combined theoretical and experimental Raman study is presented on a diphenyl bithiophene molecule known as a good candidate for the development of organic nonvolatile memory devices. Spectroscopic markers suitable to distinguish the different stable conformers of the molecule have been predicted and detected. The combined analysis of theoretical and experimental Raman spectra recorded in solution indicates that at room temperature a dynamical equilibrium, characterized by interconversion between the two more stable conformers (namely trans and cis), takes place and that the more populated species is the cis form. Referring to the solid phase instead, Raman spectra of single‐crystal samples show the presence of the only trans conformer, as confirmed by X‐ray measurements. Finally, Raman spectra of thin films, as those used for the memory device, were collected; samples just deposited from solution and after few hours from the deposition were analyzed. Following the evolution of selective spectroscopic Raman markers, an isomerization process from the abundant cis (as‐deposited) to the totally trans (after few hours) conformer in the solid phase was detected. These results open the way to the identification of the molecular isomers present in the thin film of the memory cell and finally of the active molecular species involved in the switching mechanism of the operating device. Copyright © 2009 John Wiley & Sons, Ltd.     

The pure rotational spectra of the two lowest energy conformers of the asymmetric ether C4H9OC2H5

An experimental study has been performed shedding light on the conformational energies of the asymmetric ether n-butyl ethyl ether. Rotational spectroscopy between 7.8 GHz and 16.2 GHz has identified two conformers of n-butyl ethyl ether, C₄H₉OC₂H₅. In these experiments spectra were observed as the target compound participated in an argon expansion from high to low pressure causing molecular rotational temperatures to be below 4 K. For one conformer, 95 pure rotational transitions have been recorded, for the second conformer, 20 pure rotational transitions were recorded. Rotational constants and centrifugal distortion constants are presented for both butyl ethyl ether conformers. The structures of both conformers have been identified by exploring the multi-dimensional molecular potential energy surface using ab initio calculations. From the numerous low energy conformers identified using ab initio methods, the three lowest conformers were pursued at increasingly higher levels of theory, i.e. complete basis set extrapolations, coupled cluster methods, and also taking into consideration zero point vibrational energies. The two conformers observed experimentally are only revealed to be the two lowest energy conformers when high levels of quantum chemical methodologies are employed.     

First principles prediction of the third conformer of hydrogenated BN sheet

We report, using first principles density functional calculations, the relative stabilities, structural and electronic properties of various conformers of hydrogenated BN sheet (BHNH). The already known chair and boat BHNH conformers are structurally similar to those of graphane. We propose a third BHNH conformer called ‘stirrup’ which turns out to be the most stable one, as also verified by frequency analysis. In this conformer, the B–H and N–H bonds of a hexagon alternate in 3‐up and 3‐down fashion on either side of the sheet. We also explore that any other alternative hydrogenation of the BN sheet disrupts its periodic puckered geometry and turns out to be energetically less stable. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Molecular structure,vibrational spectroscopic studies and NBO analysis of the 3,5‐dichlorophenylboronic acid molecule by the density functional method

In this study, the Fourier‐transform infrared (FT‐IR) and FT‐Raman spectra of 3,5‐dichlorophenylboronicacid (3,5‐dcpba) were recorded in the solid phase. The structural and spectroscopic analysis of the 3,5‐dichlorophenylboronic was made by using density functional harmonic calculations. There are three conformers for this molecule. The computational results diagnose the most stable conformer of 3,5‐dcpba as the ct form. The geometrical parameters and energies have been obtained for all three conformers from DFT (B3LYP) with 6‐311+ + G(d,p) basis set calculations. The vibrations of stable and unstable conformers of 3,5‐dcpba are researched by using quantum chemical calculations. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with the scaled quantum mechanics (SQM) method. The stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using the natural bond orbital (NBO) analysis. The results show that the charge in electron density (ED) in the π* and σ* antibonding orbitals and E2 energies confirms the occurrence of ıntermolecular charge transfer (ICT) within the molecule. Finally, the calculation results were applied to simulated infrared and Raman spectra of the title compound, which show agreement with the observed spectra. Copyright © 2010 John Wiley & Sons, Ltd.     

The geometry of organophosphonates: Fourier-transform microwave spectroscopy and ab initio study of diethyl methylphosphonate, diethyl ethylphosphonate, and diisopropyl methylphosphonate

The rotational spectra of diethyl methylphosphonate (DEMP), diethyl ethylphosphonate (DEEP), and diisopropyl methylphosphonate (DIMP) in supersonic expansions have been acquired using Fourier-transform microwave spectroscopy. Spectroscopic constants have been determined for five distinct conformers of the three molecules. Experimental data have been compared to ab initio calculations performed for each species. For both DEMP and DEEP, the calculations indicate the presence of several low-energy conformers (i.e., ?∼400 cm⁻¹ above the ground state) may be present at room temperature (300 K) for both DEMP and DEEP. When entrained in a supersonic expansion, the rotational temperatures of the samples are much colder (∼2 K); nonetheless, spectra from three conformers of DEEP are still observed experimentally, whereas only one conformer of DEMP is observed. In contrast, only a single low-energy conformer of DIMP is predicted by theory, and is present in the molecular beam. The relative abundance of low-energy conformers of DEMP and DEEP is attributed to the flexibility of the ethoxy groups within each molecule. The presence of multiple DEEP conformers in the supersonic beam indicates a more complex potential energy surface for this molecule that is directly related to conformational shifts of the PCH₂CH₃ group. Conversely, the absence of low-energy conformers of DIMP is attributed to steric hindrance between isopropoxy groups in the molecule. The internal rotation barrier for the PCH₃ group in DEMP and DIMP is compared to that found in DMMP and several phosphonate-based chemical weapon agents.     

REVIEW: High pressure NMR study of proteins – seeking roots for function,evolution, disease and food applications

NMR experiments at variable pressure reveal a wide range of conformation of a globular protein spanning from within the folded ensemble to the fully unfolded ensemble, herewith collectively called “high-energy conformers”. The observation of “high-energy conformers” in a wide variety of globular proteins has led to the “volume theorem”: the partial molar volume of a protein decreases with the decrease in its conformational order. Since “high-energy conformers” are intrinsically more reactive than the basic folded conformer, they could play decisive roles in all phenomena of proteins, namely function, environmental adaptation and misfolding. Based on the information on high-energy conformers and the rules on their partial volume in its monomeric state and amyloidosis, one may have a general view on what is happening on proteins under pressure. Moreover, one may even choose a high-energy conformer of a protein with pressure as variable for a particular purpose. Bridging “high-energy conformers” to macroscopic pressure effects could be a key to success in pressure application to biology, medicine, food technology and industry in the near future.     

Vibrational Analysis of 1,2-Dibromopropane and 1,2-Dibromopropane-D6

Abstract

Infrared spectra were obtained for 1,2-dibromopropane-d₆ in the liquid and in the unannealed and annealed solid states. Vibrational assignments were made for the three conformers of 1,2-dibromopropane and the three conformers of 1,2-dibromopropane-d₆ with the aid of normal coordinate calculations. All three possible conformers of CD₂BrCDBrCD₃ were found to be present in the liquid and unannealed solid, but the P_HS_HH conformer was absent in the annealed solid.     

A theoretical investigation of electronic ground state of parent sulfur diimide

In this paper various properties of parent sulfur diimides (PSD) as the simplest member of sulfur diimides family have been considered using both DFT and ab initio methods employing correlation consistent basis set hierarchies. According to these calculations, EZ conformer is predicted to be the most stable conformer in accord with experimental observation, while its energy difference with ZZ conformer is completely minute. Comparison of microwave gas phase spectra and dense phase IR experimental data with theoretical calculations show a great coincidence. The properties of EE conformer have also been anticipated and its possible presence in dense phase have been discussed although no firm experimental data exists for this conformer. The possible pathways for interconversion between various conformers have been investigated and only two unimolecular type processes namely EZ ↔ EE and EZ ↔ ZZ interconversions have been established according to a pseudo-rotation mechanism as constituting the essential dynamic of system.     

Millimeter wave spectrum of glycine

We present new investigations of the millimeter wave spectra of the two lowest-energy conformers of glycine (NH₂CH₂COOH). Measurements of these spectra have been carried out between 75 and 260 GHz using the millimeter-wave spectrometer in Kharkov. The new data set involves rotational transitions with J up to 44 and K_a up to 15 for conformer I and transitions with J up to 43 and K_a up to 14 for conformer II. This represents a more than twofold expansion both in the frequency range and J quantum-number range in comparison with previous investigations. The improved sets of spectroscopic parameters obtained for both conformers provide accurate transition frequencies for the key lines necessary for radio astronomy searches for interstellar glycine.