A chemical systems approach to evolution

A novel approach to the evolution of organisms is given. It asserts that biological evolution was consequential upon geochemical, environment, change and was inevitable not accidental.     

Toward practical quantum embedding simulation of realistic chemical systems on near-term quantum computers

Quantum computing has recently exhibited great potential in predicting chemical properties for various applications in drug discovery, material design, and catalyst optimization. Progress has been made in simulating small molecules, such as LiH and hydrogen chains of up to 12 qubits, by using quantum algorithms such as variational quantum eigensolver (VQE). Yet, originating from the limitations of the size and the fidelity of near-term quantum hardware, the accurate simulation of large realistic molecules remains a challenge. Here, integrating an adaptive energy sorting strategy and a classical computational method—the density matrix embedding theory, which respectively reduces the circuit depth and the problem size, we present a means to circumvent the limitations and demonstrate the potential of near-term quantum computers toward solving real chemical problems. We numerically test the method for the hydrogenation reaction of C₆H₈ and the equilibrium geometry of the C₁₈ molecule, using basis sets up to cc-pVDZ (at most 144 qubits). The simulation results show accuracies comparable to those of advanced quantum chemistry methods such as coupled-cluster or even full configuration interaction, while the number of qubits required is reduced by an order of magnitude (from 144 qubits to 16 qubits for the C₁₈ molecule) compared to conventional VQE. Our work implies the possibility of solving industrial chemical problems on near-term quantum devices.

Quantum embedding simulation greatly enhanced the capability of near-term quantum computers on realistic chemical systems and reach accuracy comparable to advanced quantum chemistry methods.     

Joint QSAR analysis using the Free-Wilson approach and quantum chemical parameters

A new quantitative structure-activity relationship (QSAR) technique combining the Free-Wilson method and constructed quantum chemical parameters was used to simulate the aqueous solubility (Sw), 1-octanol/water partition coefficient (Kow) of 14 new synthesized benzanilide derivatives and their 96 h acute toxicity (EC50) to Daphnia magna. The mode of action of the 14 selected compounds to Daphnia magna was shown to be a complex process involving a physical partition stage and a bio-chemical reaction stage. The results also indicated that the joint (QSAR) analysis was much effective than the original Free-Wilson method and Hansch method not only in predicting properties/toxicity, but also in investigating the mode of action of chemicals.     

Environmental effects on hydrogen bonded systems: A quantum chemical study of proton relay model systems

In this paper an application of a reaction field theory of solvent effects has been made to study proton transfer mechanisms in hydrogen bonded systems coupled to an environment. The latter is simulated with reaction fields having variable strength and direction (defined with respect to the supermolecule's total dipole moment direction), together with superposed uniform external electric fields. Changes in proton potential curves and some other properties of a model water dimer and a water trimer are reported. The results are discussed in relation to relevant phenomena in biology and biochemistry, namely proton relay systems in enzymatic catalysis.     

Multiconfigurational quantum chemical methods for molecular systems containing actinides

Recent advances in computational actinide chemistry are reported in this tutorial review. Muticonfigurational quantum chemical methods have been employed to study the gas phase spectroscopy of small actinide molecules. Examples of actinide compounds studied in solution are also presented. Finally the multiple bond in the diuranium molecule and other diactinide compounds is described.     

Molecular orbital resonance theory: A new approach to the treatment of quantum chemical problems

An alternative approach to the treatment of the quantum chemical problems combining both, the MO and VB theory, is proposed. This approach retains the concept of resonance from the VB method, but it treats each particular bond in the MO sense. The method is illustrated with a few examples. Relative stabilities of benzene, pentalene and cyclobutadiene are derived. A Hückel (4m + 2) rule is derived for the annulenes. The charge polarisation in the case of the pentalene molecule is explained. A distortion of the pentalene molecule is considered and it is shown that within this approach the distortion depends on the charge polarisation.     

A subsystem density-functional theory approach for the quantum chemical treatment of proteins

We present an extension of the frozen-density embedding (FDE) scheme within density-functional theory [T. A. Wesolowski and A. Warshel, J. Phys. Chem. 97, 8050 (1993)] that can be applied to subsystems connected by covalent bonds, as well as a practical implementation of such an extended FDE scheme. We show how the proposed scheme can be employed for quantum chemical calculations of proteins by treating each constituting amino acid as a separate subsystem. To assess the accuracy of the extended FDE scheme, we present calculations for several dipeptides and for the protein ubiquitin.     

A quantum chemical approach to the mechanism of the biochemical action of nicotinamide

The reaction of protonated nicotinamide with hydride ion, which models the transfer of hydrogen from a substrate to the nicotinamideadeninedinucleotide (NAD⁺) molecule, i.e., the principal biological function of vitamin PP, was investigated by optimization of the geometry in terms of the self-consistent field (SCF) method with allowance for configuration interaction (CI) in the PM-3 approximation. It was shown that the initial event of the reaction is electron transfer, followed by the addition of a hydrogen atom to the NAD radical. The addition product is relatively stable and has a heat of formation of −68.25 kJ/mol. The geometric structure and the distribution of charges of the reagent and also the behavior of the singlet and triplet terms in the course of the reaction were analyzed. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 35, No. 5, pp. 277–283, September–October, 1999.     

Tautomeric and conformational properties of acetoacetamide: electron diffraction and quantum chemical study

The tautomeric properties of acetoacetamide, CH3C(O)CH2C(O)NH2, have been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-31G(d,p) and 6-311++G(3df,pd) basis sets). GED results in a mixture of 63(7)% enol tautomer and 37(7)% diketo form at 74(5) degrees C. Only one enol form with the O-H bond adjacent to the methyl group (CH3C(OH)=CHC(O)NH2) and only one diketo conformer (with dihedral angles tau(O=C(CH3)-C-C) = 31.7(7.5) degrees and tau(O=C(NH2)-C(H2)-C(O)) = 130.9(4.5) degrees ) are present. The calculated tautomeric composition varies in a wide range depending on the quantum chemical method and basis set. Only the B3LYP method with small basis sets reproduces the experimental composition correctly.     

Small atomic clusters: quantum chemical research of isomeric composition and physical properties

Structural Chemistry - In this review, we give a brief summary of methodological and computational aspects of determination of structure and different size-dependent properties of small atomic...     

A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems

A computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO , AM 1, and PM 3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM /MM ) potential, a systematic study of the structures and energies of neutral and charged hydrogen-bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM /MM potential behaves better than do related MNDO /M , AM 1, and PM 3 methods. As a case in point, the draw-back of AM 1 favoring bifurcated H-bonded structures over single ones is not presented in the combined AM 1/OPLS scheme. Possible ways of improvement of the combined QM /MM potential are discussed. © 1992 John Wiley & Sons, Inc.     

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.     

Structural study of 8-azole derivatives of protoberberine alkaloids: experimental and quantum chemical approach

New derivatives of protoberberine alkaloids were prepared by nucleophilic addition of some azoles (differing in bulkiness) to the iminium functionality of the quaternary protoberberine alkaloids. Compounds were structurally characterized mainly by ¹H and ¹³C NMR spectroscopy, and the structure of 8-carbazol-1-yl-7,8-dihydroberberine was determined using single-crystal X-ray diffraction. Additionally, conformational behaviors of five derivatives varying in bulkiness of the azole moiety have been investigated by low temperature NMR spectroscopy and quantum chemical calculations. Ring current effects of pyrrole and carbazole moieties on selected ¹H NMR resonances have been characterized, visualized, and discussed.     

Search for tetrylene structures that can exhibit catalytic activity: a quantum chemical approach

We present the results of a quantum chemical study of a series of tetrylenes (silylenes, germylenes, and stannylenes), aimed at identifying structural and electronic factors affecting the width of the HOMO—LUMO energy gap. Compounds considered in this work contain atoms of Group 14 elements in both di- and tricoordinate states due to additional transannular interaction. They bear substituents bonded to the atom of the Group 14 element through atoms with and without lone electron pairs. It was found that tetrylenes stabilized by both additional transannular interaction and direct bonds between the atom of the Group 14 element and the heteroatom containing a lone electron pair (in this situation the ligand acts as n-donor) are characterized by wide HOMO—LUMO energy gaps, the gap in stannylenes always being narrower than in the related silylenes and germylenes. Localization of the HOMO and LUMO in certain tetrylenes is analyzed.

     

Spectroscopic and quantum chemical study of the properties and structure of 5-hydroxy-benzimidazole

The MNDO method has been used to calculate the heats of formation of six tautomeric forms of 5-hydroxybenzimidazole (1), their anionic and cationic forms, as well as the energetic, electronic, and structural characteristics of neutral, protonated, and deprotonated tautomers. According to the IR spectra,1 exists in the crystalline state and in CCl₄ and acetonitrile solution in the hydroxy form as two tautomers. A significant difference has been shown to exists in the EAS in acidic media of benzimidazoles, containing a benzene ring in the C² position, as compared with the spectra of benzimidazoles with alkyl substituents in this position. Spectral characteristics are given which can be used to distinguish the mono- and dianionic forms of derivatives of1.N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 117977 Moscow. P. Lumumba University of the Brotherhood of Nations, 117198 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1557–1565, July, 1992.     

Conformational properties of 1-methyl-1-germacyclohexane: low-temperature NMR and quantum chemical calculations

The conformational preference of the methyl group of 1-methyl-1-germacyclohexane was studied experimentally in solution (low-temperature ¹³C NMR) and by quantum chemical calculations (CCSD(T), MP2 and DFT methods). The NMR experiment resulted in an axial/equatorial ratio of 44/56 mol% at 114 K corresponding to an A value (A = G _ax ? G _eq) of 0.06 kcal mol^?1. An average value for ΔG _e→a ^#  = 5.0 ± 0.1 kcal mol^?1 was obtained for the temperature range 106–134 K. The experimental results are very well reproduced by the calculations. CCSD(T)/CBS calculations + thermal corrections resulted in an A value of 0.02 kcal mol^?1, whereas a ΔE value of ?0.01 kcal mol^?1 at 0 K was obtained.     

Sublimation properties of CoF(3): mass spectrometric and quantum chemical studies

The sublimation of cobalt trifluoride was studied using the Knudsen effusion method combined with mass spectrometry. The pressure of F was directly measured for decomposition of CoF(3)(s) into CoF(2)(s). The average kinetic energy of CoF(2)(+), CoF(+) and Co(+) fragment ions was determined and the relative ionisation cross section curves measured from 6 eV to 100 eV. Thermodynamic functions of gaseous CoF(3) and Co(2)F(6), were evaluated from geometrical and vibrational parameters provided from theoretical calculations. Heats of formation of CoF(3)(s), CoF(3)(g), Co(2)F(6)(g) were established as (-784 +/- 6) kJ/mol, (-565 +/- 11) kJ/mol and (-1289 +/- 22) kJ/mol, respectively.