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Experimental (Raman and IR) and computational (DFT, MP2) studies of the conformational diversity of 1-chloromethyl-1-fluorosilacyclopentane molecule
Abstract
1-chloromethyl-1-fluorosilacyclopentane (1-ClM-1-FSiCP) was synthesized for the first time and investigated by means of vibrational spectroscopy and theoretical calculations. FT-IR and Raman spectroscopic methods were implemented to collect vibrational spectra of 1-ClM-1-FSiCP. The conformational analysis was performed utilizing FT-IR matrix isolation technique and theoretical methods such as density functional theory and ab initio calculations. The spectra of the 1-ClM-1-FSiCP isolated in the argon and nitrogen matrices, were collected before and after the annealing process. During the conformational analysis the envelope (E) and twisted (T) ring shapes with the position of the fluorine atom and chloromethyl group in terms of axial/equatorial and cis/trans/gauche-/gauche+ positions were investigated utilizing MP2/aug-cc-pVTZ and DFT/B3LYP/aug-cc-pVTZ level of theory. Results indicate three stable conformers: twisted trans (global energy minimum), twisted gauche– and twisted gauche+. The potential energy surface scans were performed to trace the energy changes and the presence of transition state structures during ring conversion and rotation of the CH2Cl group.
... Structure optimization led to two stable low energy conformers, a twist-trans conformer and a gauche conformer. These structures are presented in the , -, , -, and , -planes in Figs two, slightly different gauche conformers which are referred to as gauche+ and gauche-in Ref. [8]. This work on the gauche form agrees structurally with the lower energy gauche+ conformer. ...
... If the energies are closer, this significant difference in dipole moment may mitigate the effects of the population difference and be visible in the microwave spectrum. In Ref. [8], the DFT energy differences were utilized as the basis of a Boltzmann population analysis, but it was not clear from the results whether the observation of the gauche+ and gauche-conformers supported the MP2 or B3LYP energy calculation. On the other hand, Ref. [8] does detail the observation of the twist-trans, gauche+ and gauche-conformations. ...
... In Ref. [8], the DFT energy differences were utilized as the basis of a Boltzmann population analysis, but it was not clear from the results whether the observation of the gauche+ and gauche-conformers supported the MP2 or B3LYP energy calculation. On the other hand, Ref. [8] does detail the observation of the twist-trans, gauche+ and gauche-conformations. ...
Heteroatoms constitute a very common fragment of a number of active pharmaceutical ingredients as well as excipients; from the point of view of significance, it is all the same if these are isosterically/bioisosterically replaced carbons/carbon substructures in aliphatic structures or real heterocycles [...]
The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP.
The available data on the van der Waals radii of atoms in molecules and crystals are summarized. The nature of the continuous variation in interatomic distances from van der Waals to covalent values and the mechanisms of transformations between these types of chemical bonding are discussed.
In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlöf, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic calculations (ANOs) provide an excellent description of molecular correlation effects. We report here a careful study of correlation effects in the oxygen atom, establishing that compact sets of primitive Gaussian functions effectively and efficiently describe correlation effects if the exponents of the functions are optimized in atomic correlated calculations, although the primitive (sp) functions for describing correlation effects can be taken from atomic Hartree–Fock calculations if the appropriate primitive set is used. Test calculations on oxygen‐containing molecules indicate that these primitive basis sets describe molecular correlation effects as well as the ANO sets of Almlöf and Taylor. Guided by the calculations on oxygen, basis sets for use in correlated atomic and molecular calculations were developed for all of the first row atoms from boron through neon and for hydrogen. As in the oxygen atom calculations, it was found that the incremental energy lowerings due to the addition of correlating functions fall into distinct groups. This leads to the concept of correlation consistent basis sets, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation consistent sets are given for all of the atoms considered. The most accurate sets determined in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding ANO sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estimated that this set yields 94%–97% of the total (HF+1+2) correlation energy for the atoms neon through boron.
Infrared and Raman spectra (3500-60 cm(-1)) of gas and/or liquid and solid 1-bromo-1-silacyclopentane (c-C4H8SiBrH) have been recorded and the vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twisted form. Ab initio calculations with a variety of basis sets up to MP2(full)/6-311+G(2df,2pd) predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but approximately 900 cm(-1) (5.98 kJ/mol) lower in energy than the planar conformer. Density functional theory calculations by the B3LYP method predict slightly lower energies for the two envelope forms and considerably lower energy for the planar form compared to the MP2 predictions. By utilizing the MP2(full)/6-31G(d) calculations the force constants, frequencies, infrared intensities, band contours, Raman activities, and depolarization values have been obtained to support the vibrational assignment. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.
The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
1-chloro-1-chloromethylsilacyclohexane (1-Cl-1-ClMSiCH) is a newly synthesized molecular compound whose conformational analysis was performed by means of vibrational spectroscopy and theoretical calculations. Conventional ATR-FTIR and Raman spectroscopic methods were used to obtain vibrational spectra of the liquid sample. Additionally, FTIR spectra of the compound isolated in low-temperature neon and nitrogen matrices were registered to make a complete assignment of the experimental vibrational spectral bands. All theoretically possible 38 canonical ring conformations considering axial/equatorial and cis/trans/gauche-/gauche+ positions of the Cl and CH2Cl group were analyzed by utilizing MP2 and B3LYP at aug-cc-pVTZ theory level. The most stable local energy minima were investigated in detail, with the global energy minimum structure being in the chair axial trans conformation. Detailed analysis of the potential energy surface revealed the transition states (TS) and the energy barriers. The conformational path was found to be the chair→ envelope/half-chair (TS)→ skew-boat C1→ boat (TS)→ skew-boat C2. The energy barrier for ¹C4 to ¹S3 conversion was found to be 4.94 kcal/mol while for the reverse process – it was calculated to be 0.26 kcal/mol. The vibrational analysis and the experimental spectra suggest that the four lowest energy (chair ring) conformers coexist at room temperature. The energy barrier for gauche to trans conversion is 1.15 kcal/mol for axial and 1.04 kcal/mol for equatorial conformers, and it is possible to observe these processes in low-temperature matrices.
Since 1-chloromethyl-1-fluorosilacyclohexane is a newly synthesized molecular compound its structural parameters and conformational stability is unknown. Raman and infrared vibrational spectroscopy methods were employed for analysis of this molecule. IR spectra were recorded for both gas phase and liquid sample, whereas the Raman experiments were performed in the liquid state. Additionally, low temperature matrix isolation infrared spectra were recorded after isolating the molecule in argon and nitrogen matrices. For the assignment of the experimental spectral bands, theoretical DFT/B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ calculations were performed. From the calculations it was found that 1-chloromethyl-1-fluorosilacyclohexane may exist in twelve different conformational forms out of which the chair axial trans conformer is the most stable form. However, there are three more chair type conformers – equatorial trans, equatorial gauche and axial gauche that are stable enough to be observed in the experimental spectra.
Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs–C2 equilibrium of tetrahydrofuran in the [email protected]2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the [email protected]2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.
Spherical conformational landscape model was revisited to include yet another class of cyclic compounds; the derivatives of cyclohexane. The updated model is not only capable of explaining Raman spectral features in fluxional cyclopentane but is also capable of revealing similarities between cyclopentane and cyclohexane derivatives for the first time. At the heart of the model lies the aspect of B/T ring coordinates (B/T conformational platform) that represents different levels of puckering (q). DFT-ωb97xd/6-311 + G* computations confirmed by MP2/aug cc-pVTZ computations were used to fully investigate 16 different derivatives of both cyclohexane and cyclopentane. Intrinsic reaction coordinate, IRC, computations were performed to gain insight into patterned inter-platform pathways connecting ring coordinates. These pathways revealed the coupling strength between bent/boat, B, and twist, T, ring coordinates. The coupling is found to be stronger for cyclopentane compared to cyclohexane. Some spectral features in the overlap region near 1400 cm⁻¹ show promising signs on spin–spin relaxation, T2, mechanism. The work opens up an avenue for conformational studies of medium-sized rings. Also, ongoing studies to unravel potential relationships between conformational flexibility and bioactivity of cyclic compounds are underway.
Graphic abstract
Conformationally mobile cyclic carbonic skeletons like cis-Octahydropentalenes are occurring in a number of natural products. A complete conformational analysis of cis-Octahydropentalenes reveals how some natural products populate their bioactive form. The pattern successfully explains the bioactive conformation in (+)-epi-goniofufrone and Hirsutic acid, both of which are natural products with potent bioactivity. Analysis like these are illustrative of how nature can use some special scaffolds to achieve maximal bioactivity, which in turn would fuel research in drug design.Open image in new window
Ring-puckering motion in twelve flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange- correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5h or C2v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytitcal formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.
The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to the conformational properties of furanose mono-, di-, oligo- and polymers in aqueous solvent. The set accounts for the possibility of arbitrary glycosidic linkage connectivity between units, O-alkylation as well as of different anomery. The compatibility with the already existing, pyranose-dedicated GROMOS 56A6CARBO/CARBO_R set allows to use the presently proposed extension for studying more diverse and biologically-relevant carbohydrates that exploit both pyranose and furanose units. The validation performed against the quantum-mechanical and experimental data concerning the structural and conformational features shows that the newly-developed set is capable to reproduce conformational equilibrium within the furanose ring, relative free energies of anomers, hydroxymethyl rotamers, and glycosidic linkage conformers. Additionally, the results concerning the conformation of the furanose ring with relation to the two-state model as well as other conformational features of furanose-containing saccharides are discussed.
In order to streamline the interpretation of vibrational spectra, this work introduces the use of Bayesian linear regression with automatic relevance determination as a viable approach to decompose the atomic motions along any vibrational mode as a weighted combination of displacements along chemically meaningful internal coordinates. This novel approach denominated vibrational mode automatic relevance determination (VMARD) is presented and compared with the well-established potential energy decomposition (PED) scheme. Good agreement is generally attained between the two methods. VMARD returns a decomposition of the atomic displacement using only a small number of internal coordinates, thus aiding the interpretation of the vibrational spectra. Moreover, the results show that the VMARD descriptions are resilient toward the addition of additional internal coordinates, achieving a concise description of the vibrational modes despite the use of redundant internal coordinates. Potential applications of VMARD involving the gathering of physical insights on the atomic motions along the reaction coordinate at transition state structures, as well as the improvement of theoretically predicted vibrational frequencies, are also presented under a proof-of-concept perspective.
This short update provides an overview of the capabilities that have been added to the ORCA electronic structure package (version 4.0) since publication of the first article in 2012. WIREs Comput Mol Sci 2018, 8:e1327. doi: 10.1002/wcms.1327
This article is categorized under:
• Electronic Structure Theory > Ab Initio Electronic Structure Methods
• Electronic Structure Theory > Density Functional Theory
• Software > Quantum Chemistry
The synthesis of heterocycles is arguably one of the oldest and at the same time one of the youngest disciplines of Organic Chemistry. Groundbreaking principles to form heterocycles, mainly by condensation reactions, were recognized in the beginning of the 19th century, and many of the classical reactions discovered at this time are still of great value today. In the 21st century, the wealth of synthetic methodology towards heterocycles is overwhelming, and especially catalysis as one of the cornerstone of green and sustainable chemistry has contributed in a major way to these developments. This perspective tries the impossible by discussing some recent advances in the construction of heterocycles, focusing on catalytic methodology. We are aware that we do not come close in giving adequate credit to the great creativity of chemists in the field.
This work concerns new superhydrophobic surfaces, generated by replacing long fluorocarbon chains, which bioaccumulate, with short chains whilst at the same time
retaining oleophobic properties. Here, is described the synthesis of novel original 3,4-propylenedioxythiophene derivatives containing both a short fluorocarbon chain (perfluorobutyl) and a hydrocarbon chain of various lengths (ethyl, butyl and hexyl). Superhydrophobic (contact angle water>150�) surfaces with good oleophobic properties (60� >contact angle hexadecane>80�) have been obtained by electrodeposition using cyclic voltammetry. Surprisingly, the lowest hystereses and sliding angles (Lotus effect) are obtained with the shortest alkyl chains due to the presence of microstructures made of nanofibers on the surfaces, whereas, the longest alkyl chains leads to nanosheets with high adhesion (Petal effect). Such materials are potential candidates for biomedical applications.
Theoretical computations have been carried out to calculate the potential energy functions for the out-of-plane vibrations of four cyclic silanes, and the results were compared to experimental functions determined from far-infrared data. The experimental and computed ring-puckering potential functions for 1-silacyclopent-3-ene, which are in excellent agreement, are quartic in nature with tiny barriers to planarity. Similarly, the calculated and experimental potential functions for 1,3-disilacyclopent-3-ene are nearly identical. For silacyclopentane and 1,3-disilacyclopentane the calculations predict ring-twisitng barriers of 2493 cm-1 (vs. 2110 cm-1 observed) and 1395 cm-1, respectively. The conformational energies for the bent forms were calculated to be 1467 cm-1 (vs. 1509 cm-1 observed) for the former and 878 cm-1 for the latter relative to the energy of the twist minima. One-dimensional hindered pseudorotational potential energy functions were found to work well for predicting the observed far-infrared spectra for the bending (pseudorotational) vibration.
Infrared and Raman spectra (3500–60 cm−1) of gas and/or liquid and solid 1-chloro-1-silacyclopentane (c-C4H8SiClH) have been recorded and the vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twisted form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers are saddle points with nearly the same energies but much lower in energy than the planar conformer. Density functional theory calculations by the B3LYP method predicts slightly lower energies for the two envelope forms and considerably lower for the planar form. By utilizing the MP2(full)/6–31G(d) calculations the force constants, frequencies, infrared intensities, band contours, Raman activities, and depolarization values have been obtained to support the vibrational assignment. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6–311 + G(d, p) calculations. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.
A comprehensive temperature and solvent study has been made of the 800–400 cm−1 region of the infra-red for chloro-, bromo-, and iodo-cyclopentane, and in the 1200–950 cm−1 region for cyclopentyl fluoride. In the case of the fluoride and the chloride, the results are interpreted in terms of the presence of equatorial and axial conformers, the axial conformer being more dominant. The enthalpy difference between the two conformers of cyclopentyl chloride in CS2 solution is estimated to be 0–7 ± 0.3 kcal.mole−1. The existence of equatorial and axial conformers in cyclopentyl chloride is confirmed by the presence of a similar ν(C-D) doublet in the spectrum of the α-deuterated compound.
The infra-red and Raman spectra from 4000 to 200 cm−1 of cyclopentyl fluoride, chloride, bromide and iodide are reported for the vapour, liquid, solution and solid phases and reasonably complete assignments proposed.
The complete infrared and Raman spectra of 1,1-difluoro-1-silacyclopentane and 1,1-dichloro-1-silacyclopentane have been recorded and analyzed. Furthermore, a number of the vibrational frequencies of the silacyclopentane and silacyclopentane-1, 1-d2 molecules have been reassigned.A normal coordinate calculation for each of these molecules was carried out and this demonstrated the validity of the assignments. Considerable mixing of the modes was found especially where ring vibrations and SiX2 motions were involved.
The infrared spectrum (3200–400cm−1) of the gas and the Raman spectrum (3200–50cm−1) of liquid and solid 1,1-difluoro-1-silacyclopentane and 1,1-dichloro-1-silacyclopentane have been recorded. In all of these physical states only the twisted (C2) conformer was detected. The conformational energies have been calculated with the Moller–Plesset perturbation method to the second order; MP2(Full) as well as the density functional theory by the B3LYP method utilizing a variety of basis sets up to 6-311+G(2df,2pd). All the calculations predict only the twisted form as the stable conformer of 1,1-difluoro-1-silacyclopentane with the average barrier to planarity of 2548cm−1 (30.49kJ/mol) from the MP2 calculations and a significantly lower value of 1422cm−1 (17.01kJ/mol) from the density functional calculations. Neither calculation was significantly affected by the inclusion of diffuse functions. The Cs conformer has a lower energy of 1703cm−1 (MP2) and 1334cm−1 (B3LYP) than the planar form. Thus the path between the two identical C2 conformers is by pseudorotational motion rather than through the planar form. Similar results obtain for 1,1-dichloro-1-silacyclopentane. The optimized geometry calculated with the 6-311+G(2df,2pd) basis is given together with a complete vibrational assignment for the twisted (C2) conformer. These assignments are supported by normal coordinate calculations with scaled force constants from MP2(Full)/6-31G(d) calculations. The results of these spectroscopic and theoretical studies are discussed and compared to the corresponding results for silacyclopentane.
The ground state pure rotational spectrum of silacyclopentane (SCP) has been investigated using both Fourier Transform Microwave (FTMW) and chirped pulse Fourier Transform Microwave (cp-FTMW) spectroscopies. In addition to the parent species, the spectra of the 13C, 29Si and 30Si singly-substituted isotopologues were recorded in the 6–24GHz region in natural abundance. Structural analysis confirms that the ground state has C2 symmetry and the geometric parameters determined based on heavy atom substitution include the bond distances, bond angles and dihedral angles of the SCP ring backbone.
This paper discusses the origin of barriers to rotation and inversion at the SCF and CI levels by use of the theory of atoms in molecules. The barriers are related to the changes in the attractive and repulsive potential energies through the use of the virial theorem. Rotation barriers in C2H6, CH3OH, and CH3NH2 are shown to result from an increase in the attractive potential energy and in spite of a decrease in the repulsive energy. Just the opposite behavior is found for the inversion barriers in NH3, PH3, and H3O+ and for the barrier to bending in H2O. The relative changes in energy found for the rotation barriers are anticipated for conformational changes dominated by an increase in internuclear separations, while those for the inversion barriers are typical of changes accompanied by decreases in these separations. The origins of the barriers are given in terms of the mechanical properties of the atoms. In ethane, the transformation of a S3 to a C3 symmetry axis in attaining the eclipsed geometry induces a quadrupole polarization of the density in the C-C bond, causing it to lengthen. This lengthening leads to a decrease in the magnitude of the attractive interaction of each carbon nucleus for the electronic charge in the basin of the other carbon atom, and this is the origin of the barrier. The changes in the charge distribution that determine these Changes in atomic properties are not consistent with a model that relates the barrier in this molecule to Pauli-like exchange repulsions between localized C-H bond orbitals.
The infrared spectra (3500–50cm−1) of the gas and solid and the Raman spectrum (3200–30cm−1) of liquid silacyclopentane, c-C4H8SiH2, have been recorded. Additionally the infrared spectrum (3200–400cm−1) of liquid xenon solutions has been recorded at −65 and −95°C. In all of the physical states only one conformer was detected which is the twisted C2 form. The conformational energetics have been calculated with the Møller–Plesset perturbation method to the second order, (MP2(full)) as well as with density functional theory by the B3LYP method utilizing a variety of basis sets. All of these calculations predict only one stable conformer i.e. the C2 form with an average barrier to planarity of 2558cm−1 (30.60kJ/mol) from the MP2 calculations and a significantly lower value of 1918cm−1 (22.95kJ/mol) from the DFT calculations with neither calculations being significantly effect by inclusion of diffuse functions. From the isolated SiH frequency from the SiHD isotopomer the SiH distance was calculated to be 1.486(3)Å. By utilizing the previously reported microwave rotational constants for three isotopomers (28Si,29Si, and 28Si-d2) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r0 structural parameters have been obtained. The determined heavy atom distances are: r0(SiC)=1.890(5); r0(C2C4) and (C3C5)=1.547(5); r0(C4C5)=1. 535(5)Å and the angles in degrees: ∠CSiC=95.9(5)°; ∠SiCC=103.3(5)°; ∠CCC=107.9(5)° with the two dihedral angles ∠SiCCC=−38.3(3)° and ∠CCCC=52.4(3)°. A complete vibrational assignment is given for the twisted C2 conformer for the normal species and the Si-d2 isotopomer which are supported by normal coordinate calculations utilizing scaled force constants from ab initio MP2(full)/6-31G(d) calculations. The results of these spectroscopic and theoretical studies are discussed and compared to the corresponding results for some similar molecules.
The far‐infrared spectra of silacyclopentane and its 1‐d1 and 1,1‐d2 isotopomers have been recorded and analyzed. Spectral series corresponding to the bending and twisting transitions were observed. Bend‐twist combination bands and bending overtone spectra were also detected. Kinetic energy (reciprocal reduced mass) expansions were calculated for the bending and twisting motions. These were used along with a five‐term two‐dimensional potential energy surface in the vibrational Hamiltonian in order to calculate the energy states. The basis sets were carefully generated to ensure that these levels were accurately calculated. The potential energy surface calculation does an excellent job of reproducing the 103 observed transition frequencies. The potential surface has energy minima at twist angles of 30°. The barrier to planarity is 2110±200 cm−1. The bent structure, which corresponds to a saddle point on the surface, has an energy about 1500 cm−1 above the twisted conformation.
The barrier potential to internal rotation in ethane is examined with bond‐orbital wavefunctions. It is found that reasonable values of the barrier height are obtained over a wide range of bond polarities if the wavefunction is constrained to satisfy the Pauli exclusion principle. By contrast, for a Hartree product of local nonorthogonal bond orbitals, the barrier is very sensitive to bond polarity. On integration of the Hellmann–Feynman forces from the determinantal bond‐orbital functions along a path that requires only force differences between staggered and eclipsed ethane, barrier values are calculated that closely parallel the corresponding total energy differences; use of an alternative path introduces a much larger error into the force calculation. The bond‐function results are utilized to examine the question of error cancellation in barrier calculations and for a comparison with other studies of the ethane barrier. It is concluded that the dominant contribution to the barrier is the overlap (exclusion‐principle) repulsion between closed‐shell, localized C☒H bond orbitals and that the direct electrostatic and dispersion force interaction between these orbitals is relatively unimportant.
Similar to analogous studies of other glycans, obtaining a detailed picture of the conformational preferences of furanose-containing oligosaccharides is often too complex to be addressed solely by experimental methods. Therefore, these investigations rely heavily on the tandem use of computational and experimental approaches. An experimental approach commonly exploited for analysis of furanose rings is the use of NMR spectroscopy together with a computer program, PSEUROT. The presence of additional rotational degrees of freedom, arising from the presence of a larger number of carbon-carbon bonds exocyclic to the ring, further complicates the conformational analysis of these systems. The favored orientations about these bonds have been difficult to determine experimentally due to the presence of exchangeable hydroxyl protons; thus, this remains a relatively unstudied area.
The silicon hydrides, SiHn (n = 1-4), and the entire set of H3SiX (X = Li, BeH, BH2, CH3, NH2, OH, F and Na, MgH, AlH2, SiH3, PH2, SH, Cl) molecules have been investigated by using ab initio methods. All structural parameters were optimized by use of the 3-21G and 3-21G(*) basis sets. The silyl derivatives are compared with the corresponding methyl compounds. In most cases, the equilibrium geometries of the methyl and silyl molecules are similar. The most notable exception is in silylamine, where a planar geometry is found about the nitrogen. Addition of d-functions to the second-row atoms results in a decrease in the bond lengths. The relative H3Si-X and H3C-X bond energies depend principally on the electronegativity of the group X. Since SiH3 has a higher electron affinity and a lower ionization potential than CH3, groups which are very electronegative or very electropositive have stronger bonds to silicon than carbon.
The microwave spectrum of silacyclopentane, 1-silacyclopentane-1,1-d2, and silacyclopentane-29Si has been investigated in the spectral range of 8-40 GHz. The rotational lines of five vibrational excited states of the ring-puckering mode have also been assigned and are consistent with a high barrier to pseudorotation. Both the dipole moment measurements and the isotopic data indicate that the skeletal ring of this molecule is in the "twisted" C2 conformation for the ground state. The a component of the dipole moment is 0.726 ± 0.005 D and the c component has been determined to be less than 0.01 D with a|μt| = 0.726 ± 0.006 D. The isotopic data are sufficient to determine the following parameters: ∠HSiH = 108.76 ± 0.26, r(Si-H) = 1.478 ± 0.004. Other important structural features have been estimated.
The energetic consequences of skeletal relaxation and natural bond orbital and symmetry decomposition of the barrier energy for dimethyl ether internal rotation is analysed. The largest contribution to the barrier energy is found to involve increased p character in the oxygen σ long-pair on going to the barrier top. Opening of the COC angle, occurring because of increased Pauli exchange repulsion between in-plane CH methyl orbitals is responsible for the p character increase. However, the Pauli repulsion does not contribute importantly to the barrier energy. π-interaction effects are found to give important, but not dominant barrier energy contributions.
New FTIR CO2 high resolution spectra are recorded in argon and nitrogen matrices at 11 K at high dilution. Their evolution with CO2 diffusion at higher temperature is also traced. New observations are discussed in regard to previous works. Even at high dilution (1/10 000), the temperature increase causes appearance of several bands both in argon and nitrogen. Identification of carbon dioxide dimer absorptions is tentatively proposed.
Despite the remarkable thermochemical accuracy of Kohn–Sham density-functional theories with gradient corrections for exchange-correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional containing local-spin-density, gradient, and exact-exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first- and second-row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
The infrared spectra (3200-50 cm(-1)) of the gas and solid and the Raman spectrum (3200-30 cm(-1)) of liquid and solid fluorocyclopentane, c-C5H9F, have been recorded. Additionally the infrared spectra (3200-400 cm(-1)) of liquid xenon solutions have been recorded at -65 and -95 degrees C. In all of the physical states, only the twisted C(1) conformer was detected. Ab initio calculations utilizing various basis sets up to MP2(full)/6-311+G(2df,2pd) with and without diffuse functions have been used to predict the conformational stabilities. These calculations predict only the twisted C1 conformer as the stable form. The two envelope (C(s) symmetry) forms with axial and equatorial structures were predicted to be first order saddle points with average higher energies of 75 +/- 33 and 683 +/- 44 cm(-1), respectively, from the C1 conformer but lower energies of 2442 and 1812 cm(-1), respectively, than the planar form by MP2 calculations. Similar values were obtained from the corresponding density functional theory calculations by the B3LYP method. A complete vibrational assignment is given for the twisted (C1) conformer which is supported by normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations. The adjusted r0 structural parameters have been obtained by systematically fitting the MP2(full)/6-311+G(d,p) predicted values with the rotational constants obtained from a microwave study. The determined heavy atom r0 distances in A are (C1C2) = 1.531(3), (C1C3) = 1.519(3), (C2C4) = 1.553(3), (C3C5) = 1.533(3), (C4C5) = 1.540(3), and (C1F6) = 1.411(3) and the angles in degrees are angle C3C1C2 = 105.5(5), angle C1C2C4 = 106.2(5), angle C1C3C5 = 102.9(5), angle F6C1C2 = 108.9(5), and angle F6C1C3 = 107.6(5) with a dihedral angle angle C2C4C5C3 = 25.3(3). These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.
Fundamental and applied aspects of chemically modified surfaces
- J P Blitz
- C B Little
J.P. Blitz, C.B. Little, Fundamental and applied aspects of chemically modified
surfaces, R. Soc. Chem. (1999) ISBN: 1855738228.
Theoretical calculations, far-infrared spectra and the potential energy surfaces of four cyclic silanes
- Chen
Rules for conformation nomenclature for Five-and Sixmembered rings in monosaccharides and their derivatives
- J C P Schwarz
J.C.P. Schwarz, Rules for conformation nomenclature for Five-and Sixmembered rings in monosaccharides and their derivatives, J. Chem. Soc. Chem.
Commun. (1973), doi: 10.1039/C39730 0 0 0505.
Compendium of chemical terminologythe "Gold Book
- Iupac
IUPAC, Compendium of chemical terminologythe "Gold Book", 2nd ed., Online corrected version: (2006-) "Electronegativity", 1997, doi: 10.1351/goldbook.
E01990.