Computational chemistry on a PC

We describe a package of some IBM PC programs that may find application in computer-aided molecular design. PCGEOM constructs and visualizes molecular models from bond lengths, bond angles, and dihedral angles, from Cartesian coordinates, or from stored fragments. It may prepare output files to be used as input for other programs, like CNDOB (conventional CNDO /2) or PCMEP using the bond increment (BI ) method for the calculation of molecular electrostatic potentials. PCPROT is in preparation and will use Protein Data Bank coordinates to visualize and manipulate protein molecular models. Starting from these, it will calculate electrostatic potentials using the BI method and/or monopoles adjusted to reproduce ab initio values for amino acid residues. FSCF is based on a CNDO -type approximation and uses strictly localized molecular orbitals in order to partition large molecules into a central fragment, a polarizable region, and a fully transferable environment. The partition allows one to handle relatively large systems with up to 200 atoms. To illustrate applications, we present estimation of relative inhibitory potencies of a series of substituted triazines on chicken liver dihydrofolate reductase.     

Computational experiments on dichroic effects in acetaldehyde

An ab initio calculation of dichroic vibrational band intensities has been performed for the n-π¹ transition of the carbonyl group in acetaldehyde (as a model compound) in a rigid asymmetric conformation. Results show a 10% contribution of vibrational effects adding to the electronic contributions. Different signs are effectively obtained according to the vibrational bands, which is promising for further applications. Concerning the method itself, results are analogous to those obtained for oscillator strengths.     

Computational chemistry with transputers: a direct SCF program

By using transputers it is possible to build up networks of parallel processors with varying topology. Due to the architecture of the processors it is appropriate to use the MIMD (multiple instruction multiple data) concept of parallel computing. The most suitable programming language is OCCAM. We investigate the use of transputer networks in computational chemistry, starting with the direct SCF method. The most time consuming step, the calculation of the two electron integrals is executed parallelly. Each node in the network calculates whole batches of integrals. The main program is written in OCCAM. For some large-scale arithmetic processes running on a single node, however, we used FORTRAN subroutines out of standard ab-initio programs to reduce the programming effort. Test calculations show, that the integral calculation step can be parallelized very efficiently. We observe a speed-up of almost 8 using eight network processors. Even in consideration of the scalar part of the SCF iteration, the speed-up is not less than 7.1.     

Computational experiments on the intramolecular energy flow in macromolecules

The microscopic details of the flow of energy in a single chain of polyethylene containing 300 atoms is discussed. The intramolecular dynamics of the polyethylene molecule is studied as a function of CH stretch excitation, temperature, and pressure. The rate of energy flow from CH stretching modes is found to be very rapid and irreversible, occurring on a timescale of less than 0.5 ps at low temperatures, and increases with temperature. A general characteristic two-phase energy flow behavior is observed, where there is initially a very rapid flow (due to the decay of the initial excitation) followed by a slower flow (due to energy redistribution throughout the system). The mechanism for the initial facile energy flow is shown to involve strong resonant pathways. In particular, a CH stretch/HCH bend Fermi (1:2) resonance is shown to dominate the short-time dynamics and facilitates the overall process of energy redistribution. The increase in the rate of energy flow as a function of the backbone temperature is found to be due to the increase in the density of the bath states for energy redistribution which subsequently results in the formation of new low-order resonant interactions (1:1, etc). The long-time dynamics, associated to complete redistribution of the initial CH stretch energy with all of the 894 available vibrational modes, occurs within a time of 2 ps. This timescale corresponds to the time for intramolecular redistribution. A comparison of the intramolecular redistribution time to that of intermolecular redistribution (redistribution in the condensed or solid phase as opposed to a single chain) is also made. A preliminary study of energy flow in a crystal of polyethylene (system containing 19 polyethylene chains) shows that the energy flow exhibits two very different time behaviors. The first is for the intramolecular redistribution as in the single chain study and the second is for intermolecular (chain-to-chain) redistribution. The timescale for intermolecular redistribution is found to be on the order of 0.2 ns at room temperature and pressure, about two orders of magitude larger than the intramolecular timescale.     

Computational chemistry and cheminformatics: an essay on the future

Computers have changed the way we do science. Surrounded by a sea of data and with phenomenal computing capacity, the methodology and approach to scientific problems is evolving into a partnership between experiment, theory and data analysis. Given the pace of change of the last twenty-five years, it seems folly to speculate on the future, but along with unpredictable leaps of progress there will be a continuous evolution of capability, which points to opportunities and improvements that will certainly appear as our discipline matures.     

Quantum chemistry simulation on quantum computers: theories and experiments

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.     

Thermal study of fast reactions by means of apparatus connected directly to a computer

An automated system of thermal analysis is described for the study of fast exothermic reactions (intensive burning, self-inflammation, transition from the non-equilibrium state to the equilibrium state, etc.). The system includes a complex of technical means for connecting the measuring instrument with the computer (hardware), and a special mathematical supply (software).The use of this system provides data required for thermal and chemical calculations in the high-temperature range.Two examples of DTA data-processing are presented.

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Zusammenfassung Ein automatisches Thermoanalyse-System zum Studium schneller exothermer Reaktionen (intensives Brennen, Selbstzündung, Übergang vom Nicht-Gleichgewichtszustand in den Gleichgewichtszustand usw.) wird beschrieben. Das System enthält eine Reihe technischer Vorrichtungen zur Verbindung des Meßgerätes mit dem Komputer und dem speziellen mathematischen Apparat.Die Anwendung dieses Systems ermöglicht die Ermittelung von Daten, welche zu thermischen und chemischen Berechnungen im Hochtemperatur-Bereich nötig sind.Zwei Beispiele der DTA-Datenverarbeitung werden gegeben.

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Résumé On décrit un système automatique d'analyse thermique pour l'étude de réactions exothermiques rapides (combustion intense, autoinflammation, transition de l'état de nonéquilibre à celui d'équilibre, etc....). Le système comprend un ensemble de moyens techniques pour coupler l'instrument de mesure à l'ordinateur et à l'appareillage mathématique spécial.L'utilisation de ce système permet d'obtenir les données nécessaires aux calculs des effets thermiques et chimiques dans le domaine des températures élevées.On présente deux exemples du traitement des données de l'ATD.

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MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry

The program MAPOS is a logically oriented computer program for computer-aided organic synthesis design suitable both for forward and retrosynthetic synthesis planning. It is based on the synthon model of organic chemistry, introduced by the authors. The fundamentals of the model as well as the basic algorithms are described. Examples of the use of the program are given.     

Quantum chemistry beyond Born–Oppenheimer approximation on a quantum computer: A simulated phase estimation study

We present an efficient quantum algorithm for beyond‐Born–Oppenheimer molecular energy computations. Our approach combines the quantum full configuration interaction method with the nuclear orbital plus molecular orbital method. We give the details of the algorithm and demonstrate its performance by classical simulations. Two isotopomers of the hydrogen molecule (H₂, HT) were chosen as representative examples and calculations of the lowest rotationless vibrational transition energies were simulated. © 2016 Wiley Periodicals, Inc.     

Effect of fingerprint conformation and spectral scaling on the performance of computer screen photo-assisted experiments

The use of computer screens as controlled light sources and web cameras as image detectors (the so-called computer screen photo-assisted technique, CSPT) is an ubiquitous alternative for the evaluation of colorimetric quick tests at homes or in primary care units. The performance of CSPT for such evaluations depends on several factors, from which the most relevant are the composition of illuminating sequences and the conformation of CSPT substance signatures. In this work, with the aid of a CSPT model, the effect of the construction of the substance signatures on the classification performance of different representative substance sets is studied. The correlation of illuminating colors with such classification is investigated, allowing one to determine redundancy and limitations with respect to visible spectroscopy. The concept of spectral scaling is introduced and its properties compared with standard procedures.     

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry

Summary A new and promising development in the field of computer simulation of molecular systems is the socalled thermodynamic cycle integration technique, which combines well-known results from statistical thermodynamics with powerful computer simulation methods. The basic formulas, the development and the applications in the areas of drug design, protein engineering and conformational analysis of this elegant technique are discussed.     

Droplet-based chemistry on a programmable micro-chip

We describe the manipulation of aqueous droplets in an immiscible, low-permittivity suspending medium. Such droplets may serve as carriers for not only air- and water-borne samples, contaminants, chemical reagents, viral and gene products, and cells, but also the reagents to process and characterise these samples. We present proofs-of-concept for droplet manipulation through dielectrophoresis by: (1). moving droplets on a two-dimensional array of electrodes, (2). achieving dielectrically-activated droplet injection, (3). fusing and reacting droplets, and (4). conducting a basic biological assay through a combination of these steps. A long-term goal of this research is to provide a platform fluidic processor technology that can form the core of versatile, automated, micro-scale devices to perform chemical and biological assays at or near the point of care, which will increase the availability of modern medicine to people who do not have ready access to modern medical institutions, and decrease the cost and delays associated with that lack of access.     

Exploratory experiments on the chemistry of the "glyoxylate scenario": formation of ketosugars from dihydroxyfumarate

In the context of a "glyoxylate scenario" of primordial metabolism, the reactions of dihydroxyfumarate (DHF) with reactive small molecule aldehydes (e.g., glyoxylate, formaldehyde, glycolaldehyde, and glyceraldehyde) in water were investigated and shown to form dihydroxyacetone, tetrulose, and the two pentuloses, with almost quantitative conversion. The practically clean and selective formation of ketoses in these reactions, with no detectable admixture of aldoses, stands in stark contrast to the formose reaction, where a complex mixture of linear and branched aldoses and ketoses are produced. These results suggest that the reaction of DHF with aldehydes could constitute a reasonable pathway for the formation of carbohydrates and allow for alternative potential prebiotic scenarios to the formose reaction to be considered.     

Computational study on a HS- sensing reaction utilizing a pyrylium derivative

In this paper, we present a comprehensive computational study on the hydrogen sulfide sensing mechanism in aqueous solution using a pyrylium derivative. The possible sensing mechanisms were investigated under the neutral condition and acidic condition in the gas phase and in aqueous solution. The pyrylium-thiopyrylium transformation under the neutral condition is thermodynamically unfavorable, while it is greatly facilitated in the acidic condition catalyzed by a hydronium cation. In addition, the UV-vis absorption maxima of pyryliums and thiopyryliums were investigated at the TDDFT/B3LYP/6-31G+(d,p) level. The red shift of absorption maximum from unsubstituted pyrylium and thiopyrylium to dimethylamino-substituted pyrylium and thiopyrylium as well as the red shift seen in the pyrylium-thiopyrylium transformation is interpreted in terms of the molecular orbital theory.     

Microwave-assisted cyanation of an aryl bromide directly on a metal-organic framework

A microwave-assisted postsynthetic modification (PSM) reaction on a metal-organic framework (MOF) has been realized. Cyanation of the Zr(4+)-based UiO-66-Br was achieved with CuCN and microwave irradiation to produce UiO-66-CN. This protocol represents a notable example of PSM on an aryl halide MOF producing a cyano-functionalized MOF.